Does it matter if the swapped upper is shorter?
Only thing that matters is permanent changes. If you retain the ability to put it to the originally approved configuration then nothing is needed. If you make a permanent change such as selling the approved configuration upper then the ATF suggests you contact them to make note of the change.
No engraving except builder and location on lower. Uppers can be swapped at will.
3 locations are permissible; frame, receiver or barrel.
My AR's are marked on the barrel. When the short uppers are on the lowers they are marked in accordance with appropriate CFR's. When a 16+" upper is on one of the lowers, there isn't any markings since it isn't in a NFA configuration.
Downside is that I can't borrow someone else's upper or build a new one without engraving. I intend to have the lowers marked but in no hurry.