Hiding geometry that is connected to other geometry does not 'separate' it - so it moves/deletes as one thing.
Using different on/off layers for part of some connected geometry also 'hides' it, BUT again it's still connected.
It's a recipe for madness.
Make a rectangular face.
Select the face and assign it to an 'off' layer.
Now erase one of the visible edges.
Now switch the 'face-layer' on - the face has vanished as it depended on the edge that you just erased !
Always model raw geometry on Layer0 - have it as your active layer..
To separate parts of geometry use a group [or make a component of it].
You can then hide/layer that 'container' separately from the rest - it is no longer 'connected'...
Geometry that sticks together is very useful, but when you don't what that effect put the geometry inside 'container' groups or components...