One important dimension of your measuring that is important to understand is how the length of time that you measure. Heart Rate Variability (HRV) is the variability of your heartbeats over a period of time. The standard readings (rMSSD, pNN50, etc) are based on some reading over a specific period.
That means if you are studying the effect of eating donuts on your HRV you need to ensure that reading 1 and reading 2 have approximately the same length (5 secs, 30 secs, 2 mins, etc). I prefer 30 seconds snapshots. Readings of different lengths are apples and oranges because you are getting an average over that time period.
If you eat a donut and read your HRV for 5 minutes the reading will an average for the 5. Eat the second donut a day later and read for 35 minutes you will get the average for 35 minutes. If your blood sugar changes more during the 35 minutes simply because your body has more time to digest it will look like a lower number on day 2 and you may draw wrong conclusions based on an error of measurement.
If all other variables are kept constant and you vary the measurement times you will get incompatible readings. Make sure you keep an eye on your timer and know that the similar timing of your readings are your most important source of useable measurements.