I should have added, this issue was experienced when modifying the FBS/FCS mod files. I just retried with the Standard fileset and had no issue with any of my attempts to drop a conference below 12, increase a conference above 12, create a new conference, and create a new team. I think I'll work from that as a base, and work through the names and logos myself.
I gotta say, this is the first time I've found a game that looks like it can accommodate my weird desires to bend/realign/reorganize CFB from the ground up. I am in love with how open ended this seems, given my dive into these files. Thank you for your work on the project!