Greetings Ethan & Tom,

I believe I have a possible solution as follows:
Say my Ubooquity.jar lives in a folder "Resources", so ./Resources/Ubooquity.jar
There should be a "cache" folder livin ./Resources/cache/

$ ls ./Resources/

cache/
logs/
themes/
Ubooquity.jar

$

Delete, remove, or rename the folders corresponding with the book types you are missing covers for :

$ cd ./Resources/cache/
$ rm -rf ./books/
$ rm -rf ./comics/

Then open / launch Ubooquity, navigate to "books" and/or "comics" and click "clear books database".
Launch new scan. (and "Apply and restart server" if needed).
This should rebuild the cover archive and you should be back in business with enjoying your collection.