Will repeated heating for mixing degrade the extract?

When using program 3/heat for mixing, you heat the extract (and carrier oil, if added) to 50 degrees Celcius for about 10 minutes.
Evaporation of valuable terpenes, cannabinoids and flavonoids happens at higher temperatures, so the loss from heating to 50 degrees is negligible.
Decarboxylation also happens at higher temperatures – typically from 90 degrees and up.
Most carrier oils like olive oil, MCT oil etc. do not degrade at 50 degrees either. So within reasonable limits, repeatedly heating using program 3 will not decrease the quality of your end product.