diff --git a/changelog/version-identifier-filter.dd b/changelog/version-identifier-filter.dd
index c60bb9c..57b8269 100644
--- a/changelog/version-identifier-filter.dd
+++ b/changelog/version-identifier-filter.dd
@@ -17,9 +17,9 @@
 enum debVerRE = ctRegex!`(?:^|\s)debug\s*\(\s*([^\s]*?)\s*\)`;
 ---
 
-For packages that use version identifiers in mixins or don't want to rely on
-grepping, the list of applicable version identifiers can be specified explicitly
-in the package file.
+For packages that use version identifiers in mixins or auto-generated sources,
+the list of applicable version identifiers can be specified explicitly in the
+package file.
 
 dub.json:
 ---
diff --git a/source/dub/generators/generator.d b/source/dub/generators/generator.d
index 41ee77b..6954363 100644
--- a/source/dub/generators/generator.d
+++ b/source/dub/generators/generator.d
@@ -431,6 +431,7 @@
 		import std.regex : ctRegex, matchAll;
 		import std.stdio : File;
 		import std.datetime : Clock, SysTime, UTC;
+		import dub.compilers.utils : isLinkerFile;
 		import dub.internal.vibecompat.data.json : Json, JSONException;
 
 		auto bs = &ti.buildSettings;
@@ -443,8 +444,9 @@
 			return;
 		}
 
-		// check all sources for version identifiers
-		auto srcs = chain(bs.sourceFiles, bs.importFiles, bs.stringImportFiles);
+		// check all existing source files for version identifiers
+		auto srcs = chain(bs.sourceFiles, bs.importFiles, bs.stringImportFiles)
+			.filter!(f => !f.isLinkerFile).filter!exists;
 		// try to load cached filters first
 		auto cache = ti.pack.metadataCache;
 		try