If I disconnect the battery on my MY99 to do an ECU reset, will that clear the alarm too, and thus not recognise the key fobs? Not sure if I have the pin code

 

No it wont.
I have done this many times without any ill effects but I have 99My with Signa M30 alarm. Are u sure u have M40???
Beastie

 

But won't your alarm go off when you disconnect it from the battery ?...have you got battery backup ?

 

Providing the alarm isnt armed when you disconnect the battery, it doesnt go off. It does give out a loud squeal when you reconnect the battery and may automatically rearm. Have your keyfob handy to disarm it if this happens.
Beastie