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Meh, maybe I will just buy a 1TB microsd for my tablet. Saw them on sale for $239

Is this something that happens if your library gets too big? I don't know what is considered too big, however:

Books Comics
Added/updated 0 0
Removed 0 0
Total 4713 9530

I am using the Comixology theme and I do see the folder the way I would wish. It doesn't just dumper everything into one huge location like Kavita does.

Thanks for the tip on Kavita. I do like it, but it looks like it doesn't show subfolders like Ubooquity does. I don't like having everything dumped into a single folder. My collection is sorted by folder and I can't really see me using Kavita if subfolders of a shared folder are just one big flat pile of comics. 

All scanned and everything looks great now!

UPDATE:

I rebooted, but this time I removed the shortcut from the Startup folder and manually started Ubooquity instead. It seems to be scanning better now.