Alarm problems

Hi I have a Disco TD5 that has been standing for a couple of months,I have been preparing it for MOT and everything was going well,I had an issue with the brake pedal going to the floor after pressure was held on and thanks to you all the problem was solved by replacing the master cylinder seals.Since I have done that the engine started and we bled the system shut it down,went away and the next day couldn't start the engine,the immobiliser wasn't working and the key fob isn't operating the locks,is this just coincidence and bad timing or could I have disturbed something whilst changing the master cylinder,the car wasn't locked after initial start up and key left in ignition as in garage so nothing had changed that way and I have changed batteries in the fob and still no joy,any advice welcomed,thanks John