IR Tx to bounce off the turbine, which is then Rx'd by a Daylight filtered phototransistor.???????????
is Tx "turn the LED on"?
Is Rx the output from a phototransistor?
Try to be a bit clearer we see only your words, no telepathic ability.

only strobe the Tx once flow has been detected
If the above assumptions are correct, how are you going to detcect flow if you do not activate the flow sensor ?
In many case it should be possible to detect the start of flow and then turn off; however, with the device off, how are you going to detect stop of flow?

Erik