I am wondering if this is a known problem and if there is a preferred way to work around this.

The workaround (in the scenario where you are unlinking a worked-upon file) would be to lock a file other than the one on which you are operating. All your workers should be attempting to lock $lock_file_name and only once the lock is achieved should they even begin to look at $file_name and operate on it. This allows operations such as creation and deletion of the object file which could otherwise be troublesome.

All that said, it does still sound a bit like an XY Problem perhaps along the lines of that to which brother InfiniteSilence alludes.