I've managed to sort this out.

Fortunately this occurred on a branch so I was able to create a new branch from the affected one at the point just before the mistake occurred. I could then inform people to switch to this one.

(The affected branch I've renamed with '_DoNotUse' suffix too.)

Doing this means that the file history of the affected files is no longer broken simply because this wasn't the case at the point that this new branch was made.