Okay, I'm going to try to address these problems one by one. I'll say, first of all, you have very... complex... systems. I'm honestly impressed at the stability of some of them
Holl around Etern was stirred up a bit, and the planet Nomad inside the Viet and Nistrader system I was OK with being messed up,
Remember that the converter is only working with what the system looks like at the time you export the simulation file. So large orbital changes over time will be totally ignored. Even small changes over the course of hours can't be considered, so things will never look 100% perfect.
but the moon Nomad around Nomai was completely flung around.
This was a weird one. I looked into it and it seems like a logical error on my part. In the simulation file, Nomai is considered a planet, which caused it to go through the planet section of code when it should have gone through the moon section. That shouldn't technically
be a problem, but it just so happens that they were orbiting a binary system, which broke the logic of my code. I'll look into fixing that.
One of the systems can't go around the barycenter faster than the other.
I said up above that binary orbits aren't calculated properly, including orbital period. Almost all of the orbital values for binary objects are useless, and until I find a fix, you'll have to fix that data yourself.
The moon Retror is supposed to go opposite of Prog
After a quick look, I don't immediately know what the problem here is. Space Engine is having a hard time reading Retror as a child of the system, even though it looks fine in the file. I suspect the binary object that was created between terra Flora and Prog is to blame, but I don't know why yet.
and one of the habitable moons was boiled.
Unfortunately, SE calculates all temperatures for planets. I can't do anything about this one.
Midterms are this upcoming week and I'll be gone this weekend, so give me some time to look into the other issues. Thank you for bringing them to my attention though; complex systems and edge cases like yours I couldn't have tested on my own. Even if it doesn't work perfectly, I hope it cuts out 95% of the process for converting these things from scratch.