Sorry to hear the theivin bastards got your partners bike, a major blow I know.
My mate had a similar experience, bike was c2, alarmed, immobilised, chained to another bike and a car parked in front of it, 30 yrds from his bedroom window in a QUIET cul-de-sac.
I don't know if they did this to yours but this is what happened to my mate, WARNING - incase any of you think an alarm/immobiliser is a deterant it's not(waste of time, apart from the insurance discount, it won't stop yer bike getting nicked).
Seemingly, they come round a few hours before they are going to nick it with a cordless drill and a can of expanding foam. Drill up through the rear mudguard fill the back seat compartment(where the sounder is) with foam and dissappear for a few hours to let it set. When they come back to nick it, you ain't gonna hear a thing !! BASTARDS.
I don't know what you can do about this ? hardened plate in the seat compartment, locate it somewhere else(where?) or whatever but I think irrespective of what you do, if they want it they'll get it.