Yeah, once you finish over dubbing and hit play again, it seems you can no longer remove the overdubbed layer. Hitting undo/erase doesn't do anything.
I like to record a kind of base / bed layer, and then be able to record another layer on top of that, and then play on top of all of that without recording. Then later be able to remove the top layer to get back to the base again, and add a new top layer or just play out till stop. I don't think that's achievable with the Axe-FX looper.
With other loopers it's also nice to be able to have the second recording not be the same length as the original. That way you can record say a 4 bar chord progression but then add 8 or 16 bars over top in another loop and just have the original one repeat 2 or 4 times in that same span.
Anyway, I'm not complaining too much since I see the looper as just a bonus in the Axe-FX and not its core function. So these things are nice-to-haves but I understand they're probably not that high on the priority list compared to all the sweet amp modelling improvements we've been getting