From what I gathered through what I've read and heard in interviews, the episodes were not filmed in the order they were broadcast. The BBC chose the order to broadcast placing the strongest episodes at the beginning and ending of each season. That's how they ended up with the problem with Milburn being in The Loxley Lozenge when he hadn't been introduced, because the BBC decided to run it as a special in December before the season 8 was broadcast in February and March.
Also each episode was not filmed in its entirety or even front to back. Scenes were shot according to locations and they might be working on several episodes at the same time with location shots all being done together and then all studio shots being done for those episodes. From what I've read, it appears they usually did half the season at a time.
So going back to season 6 - Whoops may have been filmed at the same time as last broadcast episodes of that series, in other words, they may have been the first episodes filmed in that season. Then the others were grouped and filmed at the next round.
That may not explain why the caps were changed, but it could explain why it appeared to change and then change back.