218td problems after flat battery

I have a 218td, its been stored for a while, battery has been off it for a while.

Would a dead battery cause a problem with the alarm/imobiliser ?

Problem im having is with a new battery the alarm side dosnt seem to be working, both of the plips are not unlocking/locking the doors, so the alarm isn't switching off, and I don't know the code for the override.

Is it possible that the alarm unit has failed as a result of the battery being off the car for so long ?

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