You're doing a lot of the same stuff I'm working on (albeit for a different league and not changing any team names). I managed to move some teams around (same teams, and none deleted) After changing the teams names to fit their position, and then editing the mini and large helmets, I also realized that the Player Cards, where you check their ATTs needed to be edited to match their team.
A couple of the "anomalies" I recall were that the Large Helmets has the 2 special "templates" outside of the 2 standard ones, and the special ones were for the Bengals and the Rams. Also when trying to change the uniforms, I struggled to edit the Chiefs to match what was requested because (IIRC) they were one special team that had like 3 diff sets of uniform color templates?
I will be working on this and hopefully done by this weekend for our CFT league. Just thought I'd share because the issues I came across (the anomalies if you will) really were time consuming to research and fix.