That seems to be how you do it. You don’t project the low level onto the high level, but the high level onto the low level. You can’t just set the topology to the base level unless it has the exact number of polygons and I think the same polygon ‘order’ or whatever it is.
Unfortunately, it never really works right, though. It’s much better to get a good geometry ready before you do your fine detailing. Not necessarily at the beginning, but certainly before you put on the finishing touchs. I learned that the hard way.
If you store a morph target then you can undo some of the areas that fail and get all spikey. Which to me is a bug, there’s just no reason for it to do that.
The other thing you can do is to hide the areas of the high res mesh you know will cause problems. Like the eyes, fingers, etc. That can save some time.
All in all, I see why 99% of the time if people are making game characters they just use zbrush for detailing and make detailed meshes in other apps first. Working from sculpt then retopologizing sounds great but in practice it does seem to be as big of a time saver as I had hoped. I’d actually say the retopology in zbrush is completely worthless, to be honest. I wasted a huge amount of time on with it and eventually just went down to maya and modo and made a base mesh using my sculpt as a reference. Zbrush seems to expect you to work a certain way, and if you step outside of that apparently you’re out of luck.
For a whole character that took me (a very novice modeler) only one day, whereas I spent about two weeks struggling with retopology and attempting to join separate pieces in zbrush.