You can alter the mesh to your heart’s content but there are a few things to be aware of:
If you have shape keys, I wouldn’t add any faces, since that will almost assuredly mess things up
You might have to fix the weight maps/vertex maps/UV Maps depending on how much you altered the mesh.
Re-edit the bone positions if you moved vertices around.
You can always make a backup of your character to use as a test subject for any alterations that you do. The beauty of Blender is that you may not have to apply any modifiers if you don’t want to – it just makes a little things easier down the road if you do.
I’m the same way… I sometimes create a hand or a foot and copy them to a new layer so that I can experiment with different shapes on the main layer. I guess I’m a packrat