Was the second thermo at the same height inside the bator? The temps are higher at the top and lower near the bottom. Also, if the glass one will go down to 32o F then calibrate it with ice and water. You can also put the other one (digital, I assume) on top of the one that controls the HVAC to see if they match. I don't want to scare you, but one time I cooked a batch of 48 eggs because my thermo AND the back-up one both were reading exactly 4o too low! I would have never known and would have probably cooked another batch of eggs if I hadn't bought a third one on impulse.
As for the eggs, keep turning them, gently, and they should be fine, but you HAVE to get your temps accurate. At least make sure the two are at the same height in the bators and let them stabilize for at least 4 hours.
This is helpful, as well (this thread is not really about hatching, but the one below is.)
https://www.backyardchickens.com/a/hatching-eggs-101