Jen,
I am not familiar with using HatchRite (I have seen it advertised, though) as an incubation medium, so my first comments are based solely on observations from the pictures. The first two pics show the eggs 4 days after oviposition - even at that time, most of them don't look "good" (not saying they are "bad", just that they seem to be showing signs of problems). The HatchRite, even in the last photo, appears to be very wet. Running at 100% humidity, at python incubation temperatures, you will get a fair amount of condensation on the lids...this can be problematic if it a) drips on the eggs themselves or b) drips back into the incubation media, making it too wet. There are many different schools of thought regarding incubation - dealing media (or lack thereof), temps, humidity levels, container type, use of lids/covers, and how to position/prepare the eggs - and any discussion on the subject will likely get you a variety of answers from which to choose.
Back to your current situation - let's start with some of the basics (you may have covered this in another thread, but I don't habitually follow this particular forum, so please bear with me...there are no wrong answers). What type of incubator are you using? What is the heat source, and how is it controlled. Where are the boxes, in relation to the heat source? It appears that you are using fairly small unventilated boxes - and you have had the lids both on, and off. When they were on, how much condensation were you getting in the boxes? Did you attempt to dry them or leave them alone? What are you using to measure temps, where are you taking your measurements, and what is the temperature? I noticed you referenced an Acu-Rite for checking humidity - is it an actual hygrometer, or just an analog gauge with low/med (normal)/high?
Personally, I would continue to incubate the eggs but, frankly, I would not hold too much hope (sorry, but better to be pleasantly surprised...they look pretty bad for just over 2 weeks - the denting doesn't concern me as much as the degree of discoloration that has been evident from the start)