The “no limits.exe” has a preplace limit of 600 cities. When you went back to 512 cities, did you simply remove the ones that you added or did you use an unaltered copy of your original map?
If you just removed the excess cities the file my still contain invalid data.
After additional experimentation, I'm having the same problem even using unmodded Conquests. I start with 512 cities. I can build about 45 more, but after that the game crashes. I've been playing using the No Raze, No City Limits, No Units Limits exe downloaded from here. I'm stumped. Any ideas?