Incidentally, I've finished the remake of 10 Taxing (Izzie Wizzie Lemmings Get Busy). I'm going to enforce the backroute in one version by cutting the builders to 12...... I don't yet know how to remove it without making it obvious, though. It wants a bit of thinking about..........
Upon further thought, I guess while ideally my suggestion makes sense, in practice it might be somewhat difficult, since most of the levels in PC Lemmings have a bit of leeway in terms of skill distribution and % to save (though of course it's definitely okay to to change those as well if need be).
Ideas to make things non-obvious might fall along the lines of this. Let's take Stepping Stone for example. (Unfortunately by talking about it I've just make things relatively obvious now, oh well.) To enforce the original solution so that the ceiling solution doesn't work, instead of preventing digging/mining by such obvious manners as one-way walls or steel areas, consider altering the ceiling to floor height so that it's just slightly more than the max safe-fall distance. Or hide some nasty traps in the ceiling that cannot be avoided.
To enforce the backroute, instead of just removing the stepping stones, keep them, but spread them out a little bit more, just enough so that you'll run out of builders. (Especially effective if you have distances of separation that are just a few pixels more than n builds, thereby causing you to "waste" most of the next build in order to reach the stepping stone.) Or add a second, higher level of stepping stones that would interfere with normal building, causing your builder to hit his head in inconvenient places.
I realize that by doing this you greatly increase the risk of introducing new backroutes by accident, but given that the levels will be playtested a bit, hopefully it'll not be too hard to catch issues. Even if in the worst case we have no choice but to fall back with making the easy-way-out, scream-in-your-face backroute-remover/enforcer quick-fixes, at least we'd had our fun trying for more subtlety.