Do you typically loose root even on an update like for .604, or just for the big ones (like 2.2)? When people rooted before the .604 update and then updated, yes, they did lose root.
Also, do you (typically...since it hasn't happened yet), still have your rooting app (EasyRoot for me) still on your phone, so you just click the root me button again? This is a little up in the air since we don't know for sure if the same rooting methods will work on 2.2. If the method of rooting is the same, then yes, the application should still work.
Finally, do you have to go back and re-set all your Autostarts and SetCPU junk, or should those settings hold through an upgrade? This, I'm not too sure about. Since they are root-only applications, I'm a little unsure, I assume they would hold up but don't quote me on that.