I just did one the other day. I didn't know either, so I just made darn sure that I didn't move the pump gear when I pulled it out.
The book did say that it's important to make sure you get as much oil as you can out of the passageway behind the oil pressure switch though (just above the high pressure pump.) Not sure I understand why on that, but I took a squirter bottle top and sucked a bunch out. That was the first one I have ever had to do, and it was actually a lot easier than I expected it to be.
It doesnt matter where the high pressure pump gear is. It isn't timed. When you lose the oil out of the High pressure system it will run like crap for a bit untill it works all the air through the system.