Is there an easy method for detecting or marking the actual sample frequency?
What file format are you passing back and forth?  The sample rate is stored in the file.  No need for a reference tone.

One of you is likely recording at a different sample rate than the other.  Probably one is recording at 44.1kHz, and the other 48kHz, or 88.2/96, etc.

Now, audio interfaces do vary in sample rate frequency.  44,100Hz can be 44,099Hz on one, and 44,0102Hz on another.  This won't throw your tuning off by any perceptible amount.  Given enough time, you can start hearing a difference.  However, if you are recording against a track already recorded, this isn't an issue.  The playback sample rate on his DAW while recording will be the same rate as the record rate.

So, if you put together a few parts and send him the files, and then he records a couple tracks and sends you the files, there should be no issue here.