I just did a thorough testing of setting changes, and found that all tested settings update with just a server reboot, instead of needing a new game save. I tested all basic changes, of ore type, difficulties, upon death dropping, escape pod despawn or not, poi regenerating or not, resources regenerating or not, auto-miners settings and more.
The only thing I found that did need a new game save file was changing the scenario, and that makes sense.
The save game files taken from Nitrado also do not load well into a private server, having issues upon trying to use them, requiring a new game and giving up on the saved game files from the rented server. I do not pretend to know why this is, just that it is.
Empyrion is currently having an issue with the 1.2 update, that I have been reading, where saved games are not saving properly, but my backups were before that time, so not to be confused with that. I hope they fix the game save issue though, as I am taking a break from the game until they do, and am done trouble shooting and testing for now.
I hope this thread helps those who are also experiencing this issue. It is a frustrating one, that seems to be limiting a lot of opportunity to make your server stand out among the many that are out there. Have fun and game on.