Hey All, circling back on this after a while, I don't think it was a permissions issue after all.
I suspect the way calibre desktop and calibre-web handle capitalization is slightly different and changes stored in metadata.db are case sensitive, so when I uploaded my library folder there were for whatever reason changes to the capitalization of author names that caused the issue.
Solved this by renaming folders and files in file manager to match what the error message was expecting, for example if the "Betty Smith" folder wasn't found, I renamed lowercase "betty smith" to "Betty Smith", after which I was able to normally use calibre-web. Had to do this for ~5-10% of books which is a pain but glad to have it working again. If anyone has found a better solution eager to hear it, scanning through the library for books with missing covers was a good indicator of where the broken links were.