You've got a headache here, because you're currently running devices on two different databases. Maybe there was a reason for this originally... but when that second BES was added, you should have simply used the existing SQL database instead of making a second one. Then you could have easily moved all users to one BES and the transporter tool would have covered all the handhelds.

I think you're going to need to pick one BES (go with the smaller installation) and wipe/re-activate those handhelds on the new "consolidated" BES.
I don't know that you'll be able to use the transporter tool twice.