So you got some of your MHRB into the Naphtha when doing the final extraction?
That means some root bark powder or material was then drifting inside the Naphtha phase?
Well ... doesnt it simply sink down again? And if you already separated both, then did it not THEN just sink down so you can separate it?
Otherwise - no I dont guess that there is any sort of *contamination*. If you then separated both in any way then you will be just left again with the Naphtha and solid MHRB. It would act like a stone in the Naphtha - just being there and not doing anything.
But how did you get the possibility for both to touch each other?
I thought Nomans TEK says to separate MHRB from the acidic soup after cooking it so you will be only left with the acidic soup, when you finally make contact with the Naphtha. But nevertheless, should not be a problem.
If you are concerned because of the yellow colour you can still dissolve it in a minimum amount of hot Naphtha and place it in the freezer again to get cleaner crystals.
In the freezer at - 20 °C Naphtha can still hold ~ 130 mg / 100 ml. So keep this in mind, if you only have 130 mg and use 100 ml for recrystallization nothing would precipitate, so in THIS case better use something like 10 ml.