Think we have fixed it. I was surprised that both fobs seemed to die at the same time but I think I might have worked out why..
Solution. Changed keyfob batteries (yep, it was that simple!).
Potential cause:
Keyfob 1. While they were fixing the car, I imagine car left unlocked but not started, so the key is constantly trying to communicate with the car, so the battery is heavily depleted over a series of days.
Keyfob 2. Since the battery was disconnected during the repair, keyfob 2 probably lost synchronisation with the alarm's rolling codes. When we tried keyfob 2, we didn't press it enough times to get it to resync and jumped to the conclusion that something deeper was amiss since both fobs now 'not working properly'.
Fingers crossed we have found the culprit, and posting this in case it helps anyone else in future.