Yeah, here is the way that I do it (it is a bit of a pain in the butt, but it’s the only way I’ve figured out to do it).
So, before you cut anything out, go to a little bit after to where you want to cut (after the end of that music cue). Write down (in Notepad or just on a piece of paper) the exact time code that a specific bar number is at (or you can sync up the beginning of a bar to a particular cut in the movie so it’s even more clear). You probably wanna put a time signature thing in the tempo track on that bar (so you can clearly see that it’s that bar because once you start cutting bars, you could be messing up the bar numbers and such). You’re not changing the time signature, but just put a time signature marker.
Anyways, then go do your business and cut your music however you want. Once you have done that, go to just after the end of that cue (but before the point that you notated above). Now you have to NOT use Time Warp. You just go into the tempo track itself and add a tempo point. And raise or lower the tempo of that point until the original point that you notated (above) is back in the same spot it originally was. It’ll take a minute or two of fine tuning that new tempo point until you get the spotting of that marker back in the right place (and you might need to make more than one tempo point so you can fine tune more carefully).
Does that make sense?