This is probably a pretty easy/stupid question for those who have dealt with it but I'm always wary of screwing around with stuff that can lock me out of a server so I will ask it anyway...

I need to temporarily turn off SSH 2FA so that I can transfer some accounts using the cpanel/WHM transfer tool.

If I go into sshd_config and set this:
ChallengeResponseAuthentication no

Plus go into pam.d/sshd and comment out the line:
auth required pam_google_authenticator.so nullok

I understand that that will disable 2FA for SSH. However, if once the transfer is completed if I reverse the process and turn those back on will my old code generator on my phone continue to work as it always did or will I have to "resync" it somehow in order to get valid codes?

Is there some other way I should do this to temporarily turn off 2FA?

hm. You might want to create a temporary (local) account for this without 2FA (just an idea - if that works).