You would have to one, make the procedural math solid. Put in the error-checking routines so that nothing comes undone, numbers-wise. And B, have a way to save those numbers in a system that would know they are no longer relevant but still important to know if they should become relevant again.
In other words, you have your randomly generated star systems all around you, you visit them all, they are all generated and running. You travel billions of lightyears away and visit another randomly generated star system. You now have two randomly generated star systems in memory, the one you are closest to is relevant and should be up and running. The other one should be in storage, not really running. The system should load the further system when the further system is no longer further away, calculate the differences in time for proper orbital alignments and such, making sure all of the space debris and soil sample caches are back in their proper place considering the amount of time past.