Intermittent Harmonics, Is there a physical explanation? I am doing some frequency analysis of a vibration signal from a spinning rotor, 

I am expecting to see peaks corresponding to the rotational frequency of the rotor. So the fundamental frequency should be ~0.7Hz, then I am assuming I should then see multiples of this corresponding to the harmonics? 



I can clearly see peaks at ~ 1.4Hz, 2.8Hz, 3.5Hz, and 4.2Hz but nothing at 2.1Hz which I cant understand

I am not sure whether the explanation for this can be explained physically or if its related to my sensor setup / analysis methods? I dont think it is related to the frequency resolution since this is around 0.03 Hz which seems suitably low. 

It seems likely to me that there is some kind of weighting to specific harmonics and the 2.1Hz harmonics is somehow damped but I can't think why this would be the case.
You have guessed it right. But before an explanation, you should make sure that your measuring setup is not the cause of this observation. 

The fact that your fundamental frequency is 0.7 Hz. does not mean that you should see all harmonics of that frequency at 1.4 Hz., 2.1. Hz, 2.8 Hz. etc...  

And furthermore, even if you would see those harmonics, their weights would most typically be different as suggested by the continuous-time Fourier series analysis of periodic waveforms.

The physical explanation is that your mechanical rotating system as a whole can be (approx) modeled as an LTI system with a self-frequency response composed of resonating or damping frequency modes... 

And it seems that at 2.1 Hz., the system is not able to vibrate enough, some damping must be happening.

Nothing further can be stated at this point with the given information.