diff --git a/doc/classes/EditorExportPlugin.xml b/doc/classes/EditorExportPlugin.xml
index bcc5745aa5b6..9ef911a68dc7 100644
--- a/doc/classes/EditorExportPlugin.xml
+++ b/doc/classes/EditorExportPlugin.xml
@@ -36,7 +36,6 @@
 			<description>
 				Customize a resource. If changes are made to it, return the same or a new resource. Otherwise, return [code]null[/code].
 				The [i]path[/i] argument is only used when customizing an actual file, otherwise this means that this resource is part of another one and it will be empty.
-				Calling [method skip] inside this callback will make the file not included in the export.
 				Implementing this method is required if [method _begin_customize_resources] returns [code]true[/code].
 			</description>
 		</method>
@@ -46,7 +45,6 @@
 			<param index="1" name="path" type="String" />
 			<description>
 				Customize a scene. If changes are made to it, return the same or a new scene. Otherwise, return [code]null[/code]. If a new scene is returned, it is up to you to dispose of the old one.
-				Calling [method skip] inside this callback will make the file not included in the export.
 				Implementing this method is required if [method _begin_customize_scenes] returns [code]true[/code].
 			</description>
 		</method>
@@ -84,9 +82,8 @@
 			<param index="1" name="type" type="String" />
 			<param index="2" name="features" type="PackedStringArray" />
 			<description>
-				Virtual method to be overridden by the user. Called for each exported file, except for imported resources (resources that have an associated [code].import[/code] file). The arguments can be used to identify the file. [param path] is the path of the file, [param type] is the [Resource] represented by the file (e.g. [PackedScene]), and [param features] is the list of features for the export.
+				Virtual method to be overridden by the user. Called for each exported file before [method _customize_resource] and [method _customize_scene]. The arguments can be used to identify the file. [param path] is the path of the file, [param type] is the [Resource] represented by the file (e.g. [PackedScene]), and [param features] is the list of features for the export.
 				Calling [method skip] inside this callback will make the file not included in the export.
-				Use [method _customize_resource] for imported resources that are not handled by this function.
 			</description>
 		</method>
 		<method name="_get_android_dependencies" qualifiers="virtual const">
@@ -235,6 +232,7 @@
 			<description>
 				Adds a custom file to be exported. [param path] is the virtual path that can be used to load the file, [param file] is the binary data of the file.
 				When called inside [method _export_file] and [param remap] is [code]true[/code], the current file will not be exported, but instead remapped to this custom file. [param remap] is ignored when called in other places.
+				[param file] will not be imported, so consider using [method _customize_resource] to remap imported resources.
 			</description>
 		</method>
 		<method name="add_ios_bundle_file">
diff --git a/editor/export/editor_export_platform.cpp b/editor/export/editor_export_platform.cpp
index 7417ff48c60e..c0646dc572c4 100644
--- a/editor/export/editor_export_platform.cpp
+++ b/editor/export/editor_export_platform.cpp
@@ -1124,29 +1124,97 @@ Error EditorExportPlatform::export_project_files(const Ref<EditorExportPreset> &
 	}
 
 	//store everything in the export medium
-	int idx = 0;
 	int total = paths.size();
+	// idx is incremented at the beginning of the paths loop to easily allow
+	// for continue statements without accidentally skipping an increment.
+	int idx = total > 0 ? -1 : 0;
 
 	for (const String &E : paths) {
+		idx++;
 		String path = E;
 		String type = ResourceLoader::get_resource_type(path);
 
-		if (FileAccess::exists(path + ".import")) {
-			// Before doing this, try to see if it can be customized.
+		bool has_import_file = FileAccess::exists(path + ".import");
+		Ref<ConfigFile> config;
+		if (has_import_file) {
+			config.instantiate();
+			err = config->load(path + ".import");
+			if (err != OK) {
+				ERR_PRINT("Could not parse: '" + path + "', not exported.");
+				continue;
+			}
+
+			String importer_type = config->get_value("remap", "importer");
+
+			if (importer_type == "skip") {
+				// Skip file.
+				continue;
+			}
+		}
+
+		bool do_export = true;
+		for (int i = 0; i < export_plugins.size(); i++) {
+			if (GDVIRTUAL_IS_OVERRIDDEN_PTR(export_plugins[i], _export_file)) {
+				export_plugins.write[i]->_export_file_script(path, type, features_psa);
+			} else {
+				export_plugins.write[i]->_export_file(path, type, features);
+			}
+			if (p_so_func) {
+				for (int j = 0; j < export_plugins[i]->shared_objects.size(); j++) {
+					err = p_so_func(p_udata, export_plugins[i]->shared_objects[j]);
+					if (err != OK) {
+						return err;
+					}
+				}
+			}
+
+			for (int j = 0; j < export_plugins[i]->extra_files.size(); j++) {
+				err = p_func(p_udata, export_plugins[i]->extra_files[j].path, export_plugins[i]->extra_files[j].data, idx, total, enc_in_filters, enc_ex_filters, key);
+				if (err != OK) {
+					return err;
+				}
+				if (export_plugins[i]->extra_files[j].remap) {
+					do_export = false; // If remap, do not.
+					path_remaps.push_back(path);
+					path_remaps.push_back(export_plugins[i]->extra_files[j].path);
+				}
+			}
+
+			if (export_plugins[i]->skipped) {
+				do_export = false;
+			}
+			export_plugins.write[i]->_clear();
+
+			if (!do_export) {
+				break;
+			}
+		}
+		if (!do_export) {
+			continue;
+		}
+
+		if (has_import_file) {
+			String importer_type = config->get_value("remap", "importer");
+
+			if (importer_type == "keep") {
+				// Just keep file as-is.
+				Vector<uint8_t> array = FileAccess::get_file_as_bytes(path);
+				err = p_func(p_udata, path, array, idx, total, enc_in_filters, enc_ex_filters, key);
+
+				if (err != OK) {
+					return err;
+				}
+
+				continue;
+			}
 
+			// Before doing this, try to see if it can be customized.
 			String export_path = _export_customize(path, customize_resources_plugins, customize_scenes_plugins, export_cache, export_base_path, false);
 
 			if (export_path != path) {
 				// It was actually customized.
 				// Since the original file is likely not recognized, just use the import system.
 
-				Ref<ConfigFile> config;
-				config.instantiate();
-				err = config->load(path + ".import");
-				if (err != OK) {
-					ERR_PRINT("Could not parse: '" + path + "', not exported.");
-					continue;
-				}
 				config->set_value("remap", "type", ResourceLoader::get_resource_type(export_path));
 
 				// Erase all Paths.
@@ -1182,33 +1250,6 @@ Error EditorExportPlatform::export_project_files(const Ref<EditorExportPreset> &
 				}
 			} else {
 				// File is imported and not customized, replace by what it imports.
-				Ref<ConfigFile> config;
-				config.instantiate();
-				err = config->load(path + ".import");
-				if (err != OK) {
-					ERR_PRINT("Could not parse: '" + path + "', not exported.");
-					continue;
-				}
-
-				String importer_type = config->get_value("remap", "importer");
-
-				if (importer_type == "skip") {
-					// Skip file.
-					continue;
-				}
-
-				if (importer_type == "keep") {
-					// Just keep file as-is.
-					Vector<uint8_t> array = FileAccess::get_file_as_bytes(path);
-					err = p_func(p_udata, path, array, idx, total, enc_in_filters, enc_ex_filters, key);
-
-					if (err != OK) {
-						return err;
-					}
-
-					continue;
-				}
-
 				List<String> remaps;
 				config->get_section_keys("remap", &remaps);
 
@@ -1270,66 +1311,24 @@ Error EditorExportPlatform::export_project_files(const Ref<EditorExportPreset> &
 			}
 
 		} else {
-			// Customize.
-
-			bool do_export = true;
-			for (int i = 0; i < export_plugins.size(); i++) {
-				if (GDVIRTUAL_IS_OVERRIDDEN_PTR(export_plugins[i], _export_file)) {
-					export_plugins.write[i]->_export_file_script(path, type, features_psa);
-				} else {
-					export_plugins.write[i]->_export_file(path, type, features);
-				}
-				if (p_so_func) {
-					for (int j = 0; j < export_plugins[i]->shared_objects.size(); j++) {
-						err = p_so_func(p_udata, export_plugins[i]->shared_objects[j]);
-						if (err != OK) {
-							return err;
-						}
-					}
-				}
-
-				for (int j = 0; j < export_plugins[i]->extra_files.size(); j++) {
-					err = p_func(p_udata, export_plugins[i]->extra_files[j].path, export_plugins[i]->extra_files[j].data, idx, total, enc_in_filters, enc_ex_filters, key);
-					if (err != OK) {
-						return err;
-					}
-					if (export_plugins[i]->extra_files[j].remap) {
-						do_export = false; //if remap, do not
-						path_remaps.push_back(path);
-						path_remaps.push_back(export_plugins[i]->extra_files[j].path);
-					}
-				}
+			// Just store it as it comes.
 
-				if (export_plugins[i]->skipped) {
-					do_export = false;
-				}
-				export_plugins.write[i]->_clear();
+			// Customization only happens if plugins did not take care of it before.
+			bool force_binary = convert_text_to_binary && (path.get_extension().to_lower() == "tres" || path.get_extension().to_lower() == "tscn");
+			String export_path = _export_customize(path, customize_resources_plugins, customize_scenes_plugins, export_cache, export_base_path, force_binary);
 
-				if (!do_export) {
-					break; //apologies, not exporting
-				}
+			if (export_path != path) {
+				// Add a remap entry.
+				path_remaps.push_back(path);
+				path_remaps.push_back(export_path);
 			}
-			//just store it as it comes
-			if (do_export) {
-				// Customization only happens if plugins did not take care of it before
-				bool force_binary = convert_text_to_binary && (path.get_extension().to_lower() == "tres" || path.get_extension().to_lower() == "tscn");
-				String export_path = _export_customize(path, customize_resources_plugins, customize_scenes_plugins, export_cache, export_base_path, force_binary);
-
-				if (export_path != path) {
-					// Add a remap entry
-					path_remaps.push_back(path);
-					path_remaps.push_back(export_path);
-				}
 
-				Vector<uint8_t> array = FileAccess::get_file_as_bytes(export_path);
-				err = p_func(p_udata, export_path, array, idx, total, enc_in_filters, enc_ex_filters, key);
-				if (err != OK) {
-					return err;
-				}
+			Vector<uint8_t> array = FileAccess::get_file_as_bytes(export_path);
+			err = p_func(p_udata, export_path, array, idx, total, enc_in_filters, enc_ex_filters, key);
+			if (err != OK) {
+				return err;
 			}
 		}
-
-		idx++;
 	}
 
 	if (convert_text_to_binary || !customize_resources_plugins.is_empty() || !customize_scenes_plugins.is_empty()) {