diff --git a/src/dune/action_unexpanded.ml b/src/dune/action_unexpanded.ml
index 4965508a23ec..8a53f0592593 100644
--- a/src/dune/action_unexpanded.ml
+++ b/src/dune/action_unexpanded.ml
@@ -380,6 +380,8 @@ end = struct
     val ( +<+ ) : outcome -> target -> outcome
 
     val ( +<! ) : outcome -> program -> outcome
+
+    val ( +<- ) : outcome -> path -> outcome
   end
 
   module Make
@@ -420,7 +422,7 @@ end = struct
       | Digest_files l -> List.fold_left l ~init:acc ~f:( +< )
       | Diff { optional; file1; file2; mode = _ } ->
         if optional then
-          acc +< file1
+          acc +< file1 +<- file2
         else
           acc +< file1 +< file2
       | Merge_files_into (sources, _extras, target) ->
@@ -466,6 +468,14 @@ end = struct
               let ( +<+ ) acc fn =
                 { acc with deps = Path.Set.add acc.deps (Path.build fn) }
 
+              let ( +<- ) acc fn =
+                match Path.as_in_build_dir fn with
+                | Some target ->
+                  { acc with
+                    targets = Path.Build.Set.remove acc.targets target
+                  }
+                | None -> acc
+
               let ( +<! ) acc prog =
                 match prog with
                 | Ok p -> acc +< p
@@ -494,6 +504,15 @@ end = struct
             { acc with deps = Path.Set.add acc.deps (Path.build fn) }
           | Unexpanded _ -> acc
 
+        let ( +<- ) acc (fn : _ String_with_vars.Partial.t) =
+          match fn with
+          | Expanded fn -> (
+            match Path.as_in_build_dir fn with
+            | Some target ->
+              { acc with targets = Path.Build.Set.remove acc.targets target }
+            | None -> acc )
+          | Unexpanded _ -> acc
+
         let ( +<! ) acc fn =
           match (fn : Partial.program) with
           | Expanded (This fn) -> { acc with deps = Path.Set.add acc.deps fn }
@@ -522,6 +541,15 @@ end = struct
             { acc with deps = Path.Set.add acc.deps (Path.build fn) }
           | Unexpanded _ -> acc
 
+        let ( +<- ) acc (fn : _ String_with_vars.Partial.t) =
+          match fn with
+          | Expanded fn -> (
+            match Path.as_in_build_dir fn with
+            | Some target ->
+              { acc with targets = Path.Build.Set.remove acc.targets target }
+            | None -> acc )
+          | Unexpanded _ -> acc
+
         let ( +<! ) acc fn =
           match (fn : Partial.program) with
           | Expanded (This fn) -> { acc with deps = Path.Set.add acc.deps fn }
@@ -584,6 +612,12 @@ end = struct
         let ( +<+ ) acc _ = acc
 
         let ( +<! ) = ( +< )
+
+        let ( +<- ) acc fn =
+          if String_with_vars.is_var fn ~name:"null" then
+            acc
+          else
+            { acc with targets = List.filter acc.targets ~f:(fun t -> t <> fn) }
       end)
 
   let unexpanded_targets t = (Unexp.infer t).targets
diff --git a/test/blackbox-tests/dune.inc b/test/blackbox-tests/dune.inc
index 42a1fef864f2..2e367fcc3629 100644
--- a/test/blackbox-tests/dune.inc
+++ b/test/blackbox-tests/dune.inc
@@ -1034,6 +1034,14 @@
    test-cases/github2848
    (progn (run dune-cram run run.t) (diff? run.t run.t.corrected)))))
 
+(rule
+ (alias github2990)
+ (deps (package dune) (source_tree test-cases/github2990))
+ (action
+  (chdir
+   test-cases/github2990
+   (progn (run dune-cram run run.t) (diff? run.t run.t.corrected)))))
+
 (rule
  (alias github3046)
  (deps (package dune) (source_tree test-cases/github3046))
@@ -2584,6 +2592,7 @@
   (alias github2629)
   (alias github2681)
   (alias github2848)
+  (alias github2990)
   (alias github3046)
   (alias github3180)
   (alias github3412)
@@ -2871,6 +2880,7 @@
   (alias github2629)
   (alias github2681)
   (alias github2848)
+  (alias github2990)
   (alias github3046)
   (alias github3180)
   (alias github3412)
diff --git a/test/blackbox-tests/test-cases/github2990/dune b/test/blackbox-tests/test-cases/github2990/dune
new file mode 100644
index 000000000000..350ebef29b9f
--- /dev/null
+++ b/test/blackbox-tests/test-cases/github2990/dune
@@ -0,0 +1,15 @@
+(executable
+ (name print)
+ (modules print))
+
+(rule
+ (with-stdout-to print.ml
+  (echo "let () = print_endline \"MESSAGE\"")))
+
+(rule
+ (alias runtest)
+ (action
+  (progn
+   (with-stdout-to output.expected (echo "MESSAGE\n"))
+   (with-stdout-to output.actual (run ./print.exe))
+   (diff? output.expected output.actual))))
diff --git a/test/blackbox-tests/test-cases/github2990/dune-project b/test/blackbox-tests/test-cases/github2990/dune-project
new file mode 100644
index 000000000000..5bbef0b4909b
--- /dev/null
+++ b/test/blackbox-tests/test-cases/github2990/dune-project
@@ -0,0 +1 @@
+(lang dune 2.5)
diff --git a/test/blackbox-tests/test-cases/github2990/run.t b/test/blackbox-tests/test-cases/github2990/run.t
new file mode 100644
index 000000000000..63e4ebbb0bf6
--- /dev/null
+++ b/test/blackbox-tests/test-cases/github2990/run.t
@@ -0,0 +1,3 @@
+Test for problem in #2990
+
+  $ dune runtest