Re: How to upgrade?
Well, I don’t know how others do it but I test the upgrade on a dev server, merge any custom that needs to have that done and upload to the live server overwriting all in mu-plugins. Same as you it seems.
The creator of bp, Andy, is creating an enhancement that is being tested now for wpmu 2.7.1 that allows auto upgrades and activation for site wide plugins in wpmu. This means ‘pushbutton’ upgrades for bp. yah!