I have the MK3 Buildings, and i have 2 buildings, where the 4chests are disapeared to give the building logo's.

The place where the 4chest should be is totaly black.
I have no idea why there gone.

Is there a waye to get the chest back, instead of producing a new building (1 mk3 building cost 5000 concrete 2000 steel. So its a waste to destory the buildings.)

Known bug, you probably placed some flooring underneath them and then removed it again (that's possible when you have water-fix installed). You'll need to build another factory building, and next time be more careful with flooring inside factory buildings.

Yes i have water-fix installed, and indeed i did some flooring. Is water-fix also the reason, that you can increase the size of the building, with plaching extra floors outside the borders? Because that is what happend and i tried cleaning it back up. (But only hours later i missed the chest, so i did not link the 2 togheter)

Btw i like the buildings, this way you can keep your factory nice and small :)

When you destory a building, or biters destory a building, is the inside also really deleted/deactivated or is that kept somewhere in the save/running in background of game?

When you destroy a building, the interior is not destroyed along with it, just in case you want to get your destroyed buildings back using a cheat command. The proper way to retire your spare buildings is just to clear them out, then put them somewhere in your world (don't destroy them), you can nest them inside each other to save space.