First, the behavior in this situation depends on the mining-diversity parameter in the blockchain. If it is over 0.5 (which we recommend in any production deployment) then any network split will cause one side of the split to stop mining blocks, while the other side of the split continues to do so.
Once the network becomes reconnected, any nodes which finds themselves on the shorter fork will switch across to the other fork. Any transactions which were in the shorter fork, but not in the longer fork, will reenter the "memory pool" of those nodes, and be transmitted to the other nodes in the network, just like any new transaction. The transactions will then be confirmed in the blockchain in due course, in the usual way.