HELL YEA, found the solution, was struggling with SL for 3 years, I basically never want SL, as I don't need to sculpt non destructively 99% of the time, but as everythign we sculpt is being stored on a paint layer by default, when deleting or doing whatever with this paint layer like toggling it off and on, the scene very often break, retopo objects explodes, sculpt layer information gets re-applied randomly on random objects ect.. 3DCoat become unusable very fast with SL.
BUT
If you simply DECIMATE (geometry>decimate) the SL info gets baked on the obejct (like it should by default until you decide you neeeed SL, like in Zbrush.) The same way like you re-sample. But as on some object re-sampling/voselizing is NOT possible, (single faced, flat no volume obejcts ect..) decimating is one way to do it, you loose your topology but whatever, this just saved me several days of work on a character that started to explode once it was nearly finsihed as I just tried to clean my layers for painting.
liok's post in Sculpt Layer with Paint Layer was marked as the answer