I've sent you a PM about getting your remote receiver virginised.
You don't need the master key to program red keys to the remote receiver so nothing to worry about there. The master key is only used to program red keys against the immobiliser which is a separate system to the remote central locking / alarm.
When you disconnect and then reconnect the battery again, the alarm returns to the same state as it was in before you disconnected the battery. If the alarm was armed then it will re-arm itself again (the siren will beep and the indicators will come on momentarily as you reconnect the battery). If the alarm was disarmed it will remain disarmed.
If you're talking about removing the ECU during welding then you don't need to actually remove it completely. Just disconnect the plugs from it. It's also safer to leave the battery connected and use a surge protector across it during welding which avoids the alternator being fried. This is what I did when I was welding mine up and I've just got one of the cheap Draper surge protectors that cost me less than £15. Some people don't bother doing any of that and haven't had any problems but I do it as a precaution and for peace of mind. As long as you make sure the earth clip of the welder is connected as close to the welding area as possible then you shouldn't really have any problems.