I'm one the ones who tried to follow this tutorial, and ended up with the same missing covers issue after the scrape.
...and yeah...I'm one of the guys who *#!!* deleted the install.bat files stupidly.... BUT for those who made that mistake, you just have to reinstall exodos by clicking the setup exodos.bat file. It wil regenerate all the games frm their respective zip, right into the !dos folder. So no worries!
I guess we should wait for Jason to build something proper, as messing with the metadata is a risky business.... So lets hope he will come up with a nice new feature to import both exodos and win3xo properly in a near future.
In any circumstance, thank you so much for LB, it really rocks, even without exodos/win3xo being supported for now.