diff --git a/edk2toolext/invocables/edk2_pr_eval.py b/edk2toolext/invocables/edk2_pr_eval.py
index 00ac282e..ad5fcb37 100644
--- a/edk2toolext/invocables/edk2_pr_eval.py
+++ b/edk2toolext/invocables/edk2_pr_eval.py
@@ -141,7 +141,7 @@ def get_packages_to_build(self, possible_packages: list) -> dict:
                 pkg = self.edk2_path_obj.GetContainingPackage(os.path.abspath(f))
 
             except Exception as e:
-                self.logger.error(f"Failed to get package for file {f}.  Exception {e}")
+                self.logger.warning(f"Failed to get package for file {f}.  Exception {e}")
                 # Ignore a file in which we fail to get the package
                 continue
 
@@ -167,7 +167,7 @@ def get_packages_to_build(self, possible_packages: list) -> dict:
                 pkg = self.edk2_path_obj.GetContainingPackage(os.path.abspath(f))
 
             except Exception as e:
-                self.logger.error(f"Failed to get package for file {f}.  Exception {e}")
+                self.logger.warning(f"Failed to get package for file {f}.  Exception {e}")
                 # Ignore a file in which we fail to get the package
                 continue
 
@@ -231,10 +231,16 @@ def _get_unique_module_infs_changed(self, files: list):
         for f in files:
             if os.path.splitext(f) in [".txt", ".md"]:  # ignore markdown and txt files
                 continue
+            try:
+                infs = self.edk2_path_obj.GetContainingModules(os.path.abspath(f))
+            except Exception as e:
+                self.logger.warning(f"Failed to get module for file {f}. Exception: {str(e)}")
+                # ignore errors.  These will occur if a module or last file in folder is deleted as part of the PR
+                continue
 
-            infs = self.edk2_path_obj.GetContainingModules(os.path.abspath(f))
             if len(infs) > 0:  # if this file is part of any INFs
                 modules.extend(infs)
+
         modules = [self.edk2_path_obj.GetEdk2RelativePathFromAbsolutePath(x) for x in set(modules)]
         logging.debug("Changed Modules: " + str(modules))
         return modules
@@ -323,7 +329,7 @@ def _is_public_file(self, filepath):
         try:
             pkg = self.edk2_path_obj.GetContainingPackage(os.path.abspath(filepath))
         except Exception as e:
-            self.logger.error(f"Failed to GetContainingPackage({filepath}).  Exception: {str(e)}")
+            self.logger.warning(f"Failed to get package for {filepath}.  Exception: {str(e)}")
             return False
 
         dec = None