It all depends on what changes you make after rooting.
Some have noted that deleting certain pre-installed apps (like Blockbuster, CityID, etc) prevented them from upgrading to 604, so missing apps may also prevent upgrading to froyo, but we'll see.
After upgrading to 2.2, you probably will lose root. Again, time will tell.
The EVO forums may give you some insight. They should have 2.2 rolling in during the next couple days, but that phone is made by HTC so not an identical situation.