@Brandon ***********
Not true Brandon.
I also have 2 passports and have travelled in and out many times changing passports.
Fly out on one pp, have a visa for the country I'm flying into in the other one. Then return to Thailand on the second pp and enter. As the passports are from two different countries they are not linked . You're right that the same fingerprints are in the system but as you're using a passport from another country the one you flew out on isn't active in the system. Although the Immigration official can see that you have 2 passports , 2 nationalities the one your using is the only one they have access to.