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For some reason I get different results using ZenCBR on a network drive. Local drives => no problems finding files in sub folders. Hope this helps.
No need for OPDS. I use Mercury browser on my iPad. It has a full screen mode. Excellent for comic reading.  I use it for all my Synology packages. Remembers your passwords to.
Problem spontaneously disappeared. Strange.
I did not test putting back the thumb.db file to reproduce the problem. I did have more then 30 cbr files containing thumb.db files who would not open. It must be a coincidence than. Recompiling the cbr file fixes the problem.
I had the same problem with some of my cbr files. Could not open them. Within Ubooquity the files have a gray book icon (for easy spotting). But I had opened the files successfully with an other comic book reader. On closer inspection of the cbr files that would not open, I found a thump.db file within the cbr archive. Probably the original scanner has copy-ed the thump.db files into the cbr archive in error, because those files are hidden under default Windows settings. Ubooquity can't open cbr files containing a thump.db file. You can use WinRar to open the cbr files and remove the thump.db file within the archive. When you remove the thump.db file WinRar will make a new cbr file and overwrites the old one. Now Ubooquity can open all my cbr files.