Hey @seanmcd, thanks for posting your question to our Community.
Are you referring to files that are set to "online-only"?
If so, I'm afraid you'd need to make them available offline first, in order to edit them.
But you can still change each file individually, so once you're done editing one file, you can make it online-only again, before you download an edit the next one, etc.
I hope this helps, but let me know if you have any questions!