I had to copy over a newer version of my library and now some of the covers are not updating. They just show as black. If I rename the files, update, rename the file back to what it was, then update again, it does work however this is very tedious. Is there a way to force a specific comic to update? The program is ignoring it for some reason even though it has no cover art generated.

If you edit a comic info you can select there a paga to be used as a cover, maybe you can try that to force a cover update. I wonder what went wrong, covers should not be missing in any situation...