I have a client who takes their thyroid meds at 4:00 am during a routine bathroom break.  Their normal reading occurs at 6:00 am.  She is receiving what I considered false positive amber / red recordings.  Has anyone observed or experienced anything similar ? 

Does this make her HRV readings abnormally high or low?

Her readings will swing daily from green to red.  On the surface, it appears as if all other variables are constant.  The thyroid med is the only thing I can think of that would alter what should be constant measurement readings.  

It's quite likely.  A feature of thyroid disorders is that they are essentially a sympathovagal imbalanced state, as thyroid hormone seems to be a regulator of the ANS.

I was wondering if her HRV was decreasing indicating a more sympathetic state, or was increasing toward parasympathetic.  Hypothyroidism has been shown to produce SNS dominance and lower HRV scores, so if her medication was bringing up her levels of active thyroid hormone to normal, then a more PNS state might be likely.  On the other hand, a hyperthyroid state also produces the same situation. In this case, you see a SNS dominance and low high frequency power (which means low PNS activity).  If her medication dose was a bit too high, she might show a lower HRV score.