no that wont do anything, the door locks have no connection to the factory immobiliser whatsoever. it may also be a crank sensor fault, so its worth a look at that, see if the wires look ok.
best thing is to get it on vag-com and see what faults come up.
one thing you could do is replace the key reader from round the ign lock, all mk3s after 96 have them. take yours out first though and check the plug as the really late ones have a different connector to the early ones.