After a hard reset of my PS4, the issue has seemed to fix itself. After the hard reset (Unplugging from all power.) I logged back into the game to randomly receive 37 of the tokens in The Pre-Sequel. I assume that this is around the amount I lost from Borderlands 2.
I had left my PS4 logged into The Pre- Sequel’s title screen in power save mode for a few days. Perhaps this issue has something to do with the system failing to write to the correct profile file? Somehow not making the transition between the two games overarching profile file due to a heavy memory load in the Ps4 Cache? Or failing to call the Borderlands 2 profile file before it tried to load the data?
Edit* Spoke too soon. The issue is back, but only erases progress since the one time it worked… I hope they fix this soon, I would like to play some BL2.