I remember having that issue back in the day when I first played Cheapo (which may have even introduced this behavior? Or was it in WinLemm too?) It confused the heck out of me, and it took me a while to understand what was going on. I thought it was a bug and restarted the game in order to restart levels.
At the same time, it's way too useful of a feature to disable by default (thereby making it extremely hard to discover).
I'm surprised that clicking the R does not cancel the replay, having that would be a good start at least (especially if the R sufficiently stands out visually). I think realistically what Lix is doing by displaying some text is a decent solution. It's slightly inelegant, but at least should leave no room for confusion.
At the same time, it's way too useful of a feature to disable by default (thereby making it extremely hard to discover).
I'm surprised that clicking the R does not cancel the replay, having that would be a good start at least (especially if the R sufficiently stands out visually). I think realistically what Lix is doing by displaying some text is a decent solution. It's slightly inelegant, but at least should leave no room for confusion.
I don't smell any backroutes here!
Before I even discovered that, I was thinking perhaps the way is to bash and then bomb around the middle so to release the other Lix to get into the other Lix's basher tunnel. 
The timing had to be right and assigning the correct Lixes the skills is very crucial here!