I don't see your problem?, there's a remote sensor and transmitter, this is the battery powered one - and you run it in deep sleep mode - waking it every so often (if you want timed sampling) or directly via a GPIO trigger. The other half, the receiver, can presumably be mains powered? - so doesn't need to be in sleep at all.
So the remote wakes up, sends it's data to the main unit, then goes back to sleep again.
The 'trick' is to work out how best to implement what you need to do - what you don't want is to be sending commands from the main unit to the remote unit, not if it's battery powered. 'If' you want to be able to change settings on the remote unit (such as sampling every ten minutes instead of five) you simply do so the next time it connects.