Your comments

The easiest way would be to set a cron job. This is how I did it on my server.



Mind you, this is is via ssh from my laptop. You can probably ignore the -headless option if you don't need it. I use it because my server is headless.
I've been having this issue for years. It's annoying as sin. I have no idea what apple is thinking with it. I don't mind using osx to read the books but I just don't even bother compiling stuff anymore. I'm a full time arch linux user anyways so I normally do all my work on there anyways so it's a non issue for me. At any rate, I'm glad I could help figure out a solution. :)
I agree. That's why I use linux to extract, remove, and recompile every one I come across. It's been annoying me for years.

I wonder if it will be feasible to implement some kind of detection/warning system for when those types of files are detected?

It'd be nice to find a way have the reader remove those files from the archive completely rather than just ignore them.
Yeah, that's what I thought. I've had that issue for years on many different readers. Removing those files always worked for me. This is the main reason I only use linux to compile books. OSX Is annoying with that .DS_Store file creation.
I've had this issue with some comics because they were created on a mac. The way I was able to fix it was to extract the book itself (on something other than osx) and delete the .DS_Store files that were in the archives and recompile them to a cbr or cbz. OSX has an annoying habit of creating those hidden files every-freaking-where and often are the first file detected by some readers so it thinks that's the cover image. Since it's not, it displays as blank in Ubooquity. Protip, windows based os's will show those files naitvely, but if you use linux to do it, any file that starts with a period makes it a hidden file. Hope it helps. If you need assistance with the process I'd be happy to lend a hand if needed.
Any chance you can delete the screenshots in the main post? I'm not allowed to edit it since the status says fixed and I just realized that the first one shows my server's i.p. Or just delete this thread all together? Thanks lol.
The purge seems to have done the trick.
That I have. I cleared all browser data. I'm doing another purge of ubooquity and it's files again to see if it fixes it. I'll keep you posted.