Echoing this. I'm not at Animus, but I've been part of Paradisa for six years where we've had the canon AU rule the entire time and...well, it's honestly never been a problem. We've never had even more than two versions of certain characters at a time. And a lot of the time? They came from canons that already knew that alternate realities could exist (like in many comics), so it was far from earth shattering. The others were like "wow that's weird!" but learned to cope with it and got awesome CR from it.

So yeah, that's my own experience. It doesn't happen to most characters because they don't have canon AUs, and if it does? Well honestly it tends to work out more positively than negatively with getting CR or having an interesting time.