Missing PDFs
I went back to some older publications in my library and found that the linked PDFs were no longer attached. It seems that this has happened to other people (https://forums.zotero.org/discussion/102677/pdfs-missing-from-my-library). How do I reverse this and prevent it from happening in the future?
All the files in your personal library are still available in your online library and would be available for download.
There are some files in your group library that have never been uploaded, so if you're trying to access those on another computer, they wouldn't be available. See Files Not Syncing for troubleshooting that.