You've effectively reached the 300 title limit. I have as well. Placed badges count toward your 300 titles (stupid I know). So when you start installing new games, your 3DS will decide to look to any badges first, if it sees you have those it will remove your badges from your home screen until your title count is at 300. once you have no more badges then it starts to make your earliest installed games disappear. They will still be there, but you'll have to delete other titles to make them visible (and accessible) again.
I really want someone that's making AuReiNAND or other CFWs with A9LH to find and remove the 300 title limit, surely it must be possible.