I have up to 64 32 x2 in 2U racks MSP430F5659 to sync and detect if present from PC Host. The master 5659 1 of 2 per 2U unit is dedicated by a hardware link. It detects the presence of the Daughter (Identical Board H/W & S/W) by monitoring a flashing run Lamp (Indicating the uP running). Upon detecting an active Run indication (Typically 1HZ but varies due to operational jobs being processed). Presumably You communicate some how with the Daughter Board, doesn't this verify it's presence? Else the suggested Interrupt Idea seems suitable.
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