It's time for another update.
The track replacement went off without a hitch, and the module merges just fine now! However, I've also found another issue that was playing into my merging problems. It turns out that, for some reason, my game/PC refuses to merge any route that has a turntable onto an existing route! And just to be sure that it was the turntable that was causing the hangs, I created a new route with just a turntable sitting in the middle, then I tried to merge it with one of my other projects, and right on queue, it hung like a condemned outlaw.
You can get around this by using the offending route as the base route and merging everything else (assuming the other routes/modules don't have a turn table) onto it.