Hmm, it would be strange for any of those mods to have problems in the later eras. All of them have their uniques in the ancient era, so theres no new code that only fires later in the game that doesnt already fire from the start.
The only common element of those three mods in particular is that all three use the fresh water feature I add. However, I do this with insert or replace so there should be no overlap problems. The Garamantes also use it from the start (unlike the other two which only use it in decisions) so if its not crashing early on it shouldnt be a problem. Coincidentally, MCs Nazca also does something similar so Id check if the problem also occurs for them. Besides that, both also save a lot of plots with saveutils. My Sioux do the same (but on a larger scale) so Id check if the Sioux also have problems to test if thats the cause.
Otherwise, Im not sure. Posting logs and database entries would be helpful. I dont use CBP so I cant say if its a specific interaction. From my knowledge of it, though, theres nothing specific about the CBP late game that should cause such a conflict.
The Garamantes are getting an update soon. Since I've basically re-built the mod from scratch, if they are the problem, it should be fixed in the near future.