Do not try to separate. Leave alone, I know somtimes they pile up high and you may have to dig some incubation medium out to fit in the shoebox container, but they will be fine. You can accidentally tear the eggshell unless they are fresh, but then they may turn or roll over killing the snakes inside. And if some are separate and questionable, try incubating them anyway. I like to cut straws and place pins around loose ones to prevent any rolling.
I also separate right before they pip or get cut, but the magical glue stuff that holds them together, goes away about the same time they start dimpling so that is easy! I like to separate but then place them so they are all touching each other, I kind of think it helps signal the rest to come out when the first few do. Silly superstition maybe, but I always do it!
Separating allows you to candle and turn the embryo to the optimal position facing upward. It also allows you to remove any infertile eggs. From what I understand bad eggs wont hurt the other good eggs during the incubation process so no big deal. They do get stinky though.
Last season I only had two clutches but I found them both very quickly after they laid so I separated and candled them. This season I had one clutch that I found late and just left them stuck together. I plan to separate subsequent clutches unless I find them late and they aren’t easy to separate.
I’ve had a few incubation issues in the past and I noticed that whenever there were temperature spikes or humidity issues, the eggs that were underneath other eggs were almost always the ones that went bad.
Over the years I’ve refined my incubation methods and I haven’t had any incubation issues lately, but I still like to separate any eggs that are on top of others, just in case. (I don’t separate eggs that are side-by-side, never had any issues with those.) As long as you are careful and peel them apart slowly it’s completely possible to separate them without damaging the eggs. I’ve never ripped into an egg while separating them.
That said, I feel that it’s all a matter of personal preference. I know a lot of people like to leave them as they’re laid and that’s perfectly fine! Do whatever you feel is right for your collection.
If you decide to separate, remember to roll the eggs inward from all directions when separating. If you notice the shell start to tear work from the opposite direction. I’ve also seen people use dental floss to separate eggs but flossing them apart.
Tip* Keep a few extra egg shells after babies have hatched. If you tear an egg open, wet the already hatch egg, cut a piece and stick it over the tear. The eggs will naturally adhere to each other and seal the hole.
True, also PVA glue has been useful in closing holes.I have found if its early but not that early, wetting the eggs can loosen them a bit more too.
Mistakes happen., I could only be confident if i got them early enough in the past when the glue had not set. Too late and I found the setting of the glue would at least (if not make tares) would cause the removal of some of the outer shell and making it rough at that point which encouraged mould.
Just my experience.