This has happened to me a few times. I do interviews for magazines. I interview people, write it all down, and then compose my piece based on our conversation. I send them a draft and ask them if they want changes, please use track changes or mark them red.
Occasionally they rewrite it. One time, the piece I got back was completely unusable and no longer met the editor's spec. I took it up with the PR officer who had a chat with my interviewee and confirmed I could use my original.
Recently, someone did change a lot, and it looked awful, but in reality it wasn't that bad, so I let it go.
Bottom line, these things are about them. They're doing us a favour by cooperating, so I feel I have to be as considerate to their wishes as possible, even when they change their tune between interview and draft!
I actually felt a bit bad about the second one described, because while she'd tinkered with it a lot, the thing still basically was a lot like what I'd written, so it wasn't ruined, but because she didn't use track changes, she'd tried to mark all new entries green and all deletions red, and it was a horrendous mess that must have taken ages.
It was fine. I wished I'd not asked her to mark it red, because it created a lot of unnecessary work for her. I only expected one or two tweaks.
Sometimes we have to let the interviewees do their thing... as long as it fits the brief. But yes, oh gosh, always keep the original. They always get an email copy. I don't ever use a shared drive.