Quote:
Originally Posted by MrJamesEMcBride
Thank you so much for the help, guys! Welp, it looks like I DID screw myself over royally. There are a ton of books that I deleted that I didnt have any other formats of. At least now, I can look at the ones that are missing and seek to replace them.
Grrrrr....the things we do in a moment of stupidity 
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NO MAJOR ISSUE.... Yet

(other than if you deleted cover.jpg That one is gone because Calibre does NOT immediately embed that into the LIBRARIES COPY. The one in the book may be different. But we can cover

that )
DO NOT TRY THINGS without discussion here first. We might have a way to retrieve some, that will disappear if you do other things in the mean time
To restore those missing OPF (from the current metadata being show. Which they should have matched)
Right click the Library Icon: Library Maintenance: Check Library Backup Status: Click the Queue All Books... Button
Note this is quite a "grinder". It will run for quite a while depending on the size of your library. The Amount To Go shows above the button.
Let'r rip, and you can do anything else while it happens in background (with calibre running).
ON to your cover problem
In the Search bar:
Code:
formats:true and cover:false
That finds those books with formats, BUT that CALIBRE has no cover to show

This may
not work in your case, because you used the OS to remove the covers: Calibre does NOT know this.
NEVER CHANGE anything in the LIBRARY FOLDERS using the OS. Calibre is really showing you the log view of the stuff it has done.
OK, Tell us more about some of those WITH FORMATS, that you deleted the covers using the OS
(I do have a way to create an missing cover Error Log file, but that is just a LOG)