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Mods that only change flags don't seem to affect the checksum at all.
 
Graphics, localisation and music WON'T change checksum. Basically every mod that makes changes in common, event, decision, history and/or map WILL.

Good to know, thanks :)
 
FWIW, here are the non-overhaul/TC mods I have, and whether or not they change the checksum, and therefore disable achievements:

ARKOpack Armoiries: Yes
Better Mountains: Yes
CKII UI Font Mod: No
Climate Classification: Yes
Cultural Cities: Yes
Cultural Cities (compatible): No
Cultures and Portraits Revamp: Yes
Keyboard Shortcuts+Interface Adjust: No
Minimap (Emboss): No
NBRT+ (0.6): No*
NBRT+ (0.7): Yes*
Portrait_Realignment: Yes


* NBRT+ has been discontinued, but I had a backup of the last two versions. NBRT+V0.7 changed the checksum, due to what looks to be a new trees.bmp in /map
 
interface files also don't affect checksum. most map files too.