If by external drives you mean usb or disc, it is possible that the files ended up being read only - especially if from disc. If that's not it and Trusted Locations is not it (a common oversight when a new drive comes into the picture) then it's anyone's guess.
Too bad you didn't pay attention to a message that you were probably not used to seeing. If you got it every time, I get why you might blow through messages that you might take for granted as being the same ones. However, if it was a new thing, I don't get it and never have. Used to drive me nuts when a user would say 'it's not working - there was an error message' and I'd ask what did it say? I dunno, I didn't read it. Really??
You have backups you can fall back to? What about the ones on the temp drive? Surely you copied them back and didn't cut/paste or otherwise delete?
The more we hear silence, the more we begin to think about our value in this universe.
Paraphrase of Professor Brian Cox.