diff --git a/codecov_cli/services/upload/upload_collector.py b/codecov_cli/services/upload/upload_collector.py
index 22310e2f..207a4d43 100644
--- a/codecov_cli/services/upload/upload_collector.py
+++ b/codecov_cli/services/upload/upload_collector.py
@@ -145,6 +145,10 @@ def _get_file_fixes(
             )
         except IsADirectoryError:
             logger.info(f"Skipping {filename}, found a directory not a file")
+        except FileNotFoundError:
+            logger.warning(
+                f"File {filename} is tracked by git but was not found on disk. File fixes were not applied to this file."
+            )
 
         return UploadCollectionResultFileFixer(
             path, fixed_lines_without_reason, fixed_lines_with_reason, eof