It seems as if you’re describing an error where you had an audio file on the timeline (event is what it’s called I suppose) and it was cut by mistake. The way to fix it is of course to undo what you did. If that doesn’t work, maybe because your undo-“chain” is too long and will undo other things, then I think the only reasonable alternative is to bounce the events (“consolidate” in PT language).
By “bouncing” you get a new consolidated single audio file of the desired selected events. Of course this increases how much storage you use, but I don’t see another way of getting it done really.