(Well, actually, it would affect file syncing, but it'd just make the initial sync a bit slower while Zotero checked all files to see if they actually changed, so it's not too big a deal. But in general you should be using an automated, full-disk backup program.)

I guess the PDFs weren't in the backup folder. Lost cause but thank for all the help.

Just wondering whether there could be a reason for why the PDFs would not have transferred into the storage folder of Zotero? I inputted them and used them in Zotero regularly but, for whatever reason, they were no longer found in storage.

Did you search the backup folder itself for a few of the PDFs you're looking for?

I can't tell you why the files didn't get uploaded. It's not entirely clear that they all existed to begin with (or else why wouldn't they be in the backup folder? though the same could be said for the zotero.sqlite file...). It's possible that some security software on your system somehow interfered with the saving of the files, or it could have been an issue with your sync settings (if, say, you were previously using WebDAV syncing, though that shouldn't really matter — Zotero should recheck all files when you switch modes).

Going forward, I'd just make sure that newly downloaded files are accessible and that they show up on zotero.org after a sync.