I've got a similiar problem to Wilkin. I was playing a save file using the previous version of CPP with EUI (I noticed the new patch being put up, but since I was using quite a lot of mods at once I decided to not patch until I'm done with that file), and yesterday I found that the game inexplicably CTDs with no error messages at the end of turn 139/start of 140, around barbarian turn.
I decided to give up on that save, updated CPP and flushed cache, and started a new run. It started off no problem and I kept play until around turn 60, then saved and closed the game. Then this morning I tried to load the same mods, but the game again CTDs while loading mods (didn't even reach the screen where I can choose to load or start a new game) with no errors. Messed around with combinations a bit, turns out it only CTDs if the CPP and Battleship Girls are activated at the same time (Battleship Girls on its own caused no problems). This was puzzling since it was working just fine just the day before, and its change log on the Steam Workshop showed no updates for the last several months. Tried flushing cache and waiting for Civ to re-config it a few times, no dice.
So once again I abandoned another save, and started a new scenario with much fewer mods, consisting of only all CPP mods, the Madoka Wish For The World mod from the recommended list, the Etria Alliance mod, and Gedemon's Custom Advanced Setup Screen mod. Once again, it worked perfectly fine at first, until I saved and closed the game. This time, the game CTDs while loading the save file.
Has this problem happened to anyone else before, and is there a known way to fix it? When I installed the latest CPP patch (with EUI) with the installer, I only flushed the cache folder and didn't delete the previous version from the Mods and DLC folders, might that have caused this problem?
Also, a few overall hiccups: EUI (or perhaps CPP in general?) replaces every yield icon for tiles on the map with the food icon, even though yield icons are correct everywhere else. I generally remember which tile should yield what and can hover my mouse over them to see the correct yield so it doesn't impend me much, but it's still odd to see. Additionally, when playing without CPP, information about every building just displays variable names and values (for example "LandRouteModifier" or something like that, not the exact wording), but doesn't actually show a description of the building that can be understood without looking at game files. Fortunately Civilopedia is unaffected so the game is still perfectly playable, but knowing how to fix this would still be very nice. With every CPP mod activated, some of the options on the City-State diplomacy menu don't have descriptions (specifically Pledge to Protect and Diplomatic Marriage, and there are two copies of the latter), and clicking them has no obvious effect. Sometimes it does turn out that I've successfully pledged to protect the City-State when I end turn and check again, sometimes it didn't work.
Edit: I've really been enjoying CPP, by the way, especially the revamps to the religious/culture/science trees. It really helps justify my tendency to "even out" my tech progression, and there are enough Pantheon options that aren't weirdly situational for the latecomers to pick. Keep up the good work!