The best way is to measure temps before (ideally over at least 1-2 hours), then to measure temps the same amount of time after and compare.

In the case of this Rb oscillator, it is temperature sensitive, but also built for pretty extreme environments.

I'm not too worried about this particular application, because the clock will be in an air conditioned environment, and I'm monitoring the clock accuracy to +/- 2ns from another GPSDO / rubidium clock. The performance before and after the fan swap is within my measurement noise for 24H, though I haven't done 30+ day measurements and ADEV comparison. Still working on a consistent test setup.