Yes, if you want to upload a new version of a file and it tells you Permission Denied, you could change the permission on that file or just delete it. It could also be the directory permissions that are the problem.
But I don't see any apc.php in the upload files for the vb4.2.2 patch 4, and it doesn't seem to be a part of the full package either, so I'm not sure why you'd be uploading it when installing a patch.
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