My best guess is that, because of testing reasons, I modified "vnactor.ini", and activated ExportChara_CharaEditor, ExportChara_CharaEditorBody & ExportChara_CharaEditorCloth
At some point, because of crippling bugs, I downgrade to Version 39.0 and leave default settings, but because the scene was already saved with those previous settings, it keeps them activated without me realizing it, either that or v39 keeps them on by default, I don't know.
I checked ini, and everything was okay, but when I checked inside VNGE, I found this..!
View attachment 2317293
those settings were active.
In other words, every single scene has clothing and body saved from that char, that's why when you replace and change a scene, it reloads the body and clothing data already saved in that scene.
The only solution is to replace the char and resave it in every single scene.
Sorry, my bad