I have the same issue (I posted on this once before and I've seen occasional other posts on it but I've not seen it addressed although I may well have missed a response). I was hoping this would have been addressed in v2.1, but that seems not to have happened. For example, in the last week the app and the website show my HRV to be the same color 5 out of 7 days. Differences occur on Wed Aug 28 and Sat Aug 30 (yesterday). On Wed the app shows HRV to be amber and the website shows green and Saturday (yesterday) the app shows my HRV to be amber and the website shows green. I rely on the app to help make the call regarding training that day or not.
It would be great to see a comment from Joel on this one (apologies if this is one of those that has been asked/answered before; I did a quick search of the forums and did not see it answered).
Is there any update on this? I just started measuring my HRV a few days ago and my application and website readiness are always different. Not sure which one to listen to.