Sorry if this is already known, but I didn't see it listed here.
If you have a full party and Boxes in XD (only possible by evolving a lot of Nincada), when you obtain one of the Mt. Battle Johto starters, everything in your PC except Shadow Pokémon will be deleted to make room for it.
Note that I haven't tried this myself (or even played XD). According to the same source
, if you would obtain Ho-Oh with full PC/Boxes you instead are just told to come back another time.