I'm still reading through Age of Worms (in Chapter 8 right now). How did people deal with the whole issue in the "Free City" and the "abduction"? How did that go over with the rest of the party/players?
I ran AoW twice, once in 3.5, once in 5e. I assume the adventure you are referring to is "The Hall of Harsh Reflections"? For me, the two groups had quite different experiences. The first time around, I maybe didn't give it enough thought before hand; I don't think I did an early switch because I didn't think my players would be into it, and when it got the the 'abduction' piece, I'm not sure it had a great impact on the players; I tried to get them confused as to who was what but not sure I pulled it off. I'd say it's not written especially well, you need to think it through before hand, in the context of your players.
The second time around, I introduced an aspect of 'abduction' / 'replacement' right from the time just before the party even got into the complex; there was an ambush, in fog, in the alleyways outside, and PC's were all over the place and from memory one player might have been away, so I planted a 'proxy' right there, no worries, and told the player before they came back (a couple of my players these days are totally fine with a short-term double-cross or similar). It was kind of hard for the player to try and make it work, but it did work... as best it could. The final show-down, once again, didn't play out as well as one might expect.
I certainly think the designer tried to make a good job of the classic 'switcheroo', however it's an old trope and one that works better in a novel than in a face to face RPG. At the end of the day, the players just want to play their characters, kill things and take their stuff; back-stabbing is just an annoyance until they work out who to kill.
That said, there are actually a lot of very good things about the adventure, I rate it highly especially as it's actually just a big dungeon crawl.
