Came with the bike and are in the little jockey box on the right hand side.For those out there with a 2005 or 2006 Sprint- did the locks/keys for your Triumph hard bags come with the bike, or were they shipped separately with the hard bags when they finally arrived?
FirSTeve, if I understand you correctly, you have 2 panniers that came with your bike and have locks that are matched with the ignition key. The dealer is ordering 3 lock sets (can't order 1 or you need all 3?), of which 1 will go on the top box.
If this is correct, then you only need to wait until the lock sets come in and take one to a locksmith to change them over to work with your ignition key. Then everything matches.
It sounds to me, however, like you want to use the top box right now without waiting for the new lock sets to come in, hence the "borrowing" from the panniers. If this so, I would recommend you consider what Fullchat said about removal being a drastic measure, and wait for the replacement.
IMHO, a lot of bikes on this forum have been screwed up because someone was "in a hurry", only to have to do it again the correct way, sometimes at great expense.