I made another test with Luxury Bananas and it still works for me.
I have posted detailed information about how to find an issue on civfanatics, if you are still interested.

I also left a message on civ fanatics talking about this problem. See your LS civilization series post

I was using a mod where bananas as counted as a luxury resource. I tried to reverse sugarcane to banana and the game crashes

I am not gonna be able to do anything in this case, mods sometimes work differently on invidual machines. I recommend to simply disable this mod. If you are still interested in other civilizations, you can remove/disable Afonso in the mods folder.
If you are using dll any mod, please leave the name, I may check if there is a fatal interaction.
If you were replacing sugarcane with other modded resource, then let me know as well.
I have just tested it (v5 of mod) and it works perfectly on my pc.
Sorry for ruined game.

Everytime I try to replace sugarcane with the resoruce, the game crashes.

Philip II, you look like you got a down grade...

Nice! You are my favorite modmaker! Thanks for all your work!