Every time you repair a module, it powers off, this includes Life Support. Same with reboot repair, it shuts all modules down for a brief time, and will also consume emergency oxygen during the process.
Do this enough times without refilling life support, and you’ll suffocate, resulting in a destroyed ship.
You do not often see the remaining air when doing a simple repair with an AFMU, as you’re probably focused on the module panel.
Just in case there is a bug, I’d advise against repairing your life support module unless you absolutely have to. Having just returned from a long trip myself, I can confirm that FSD repairs don’t blow you up from what I can tell.