I can't wait to see how your new 'load settings from sim files' feature is going to turn out, because I got pissed off the other night when I ran my sim and found out my Chainbot243tC had been completely replaced by Tiebot243tC, with the chainbot's green color, and turned autotroph too!
In the mean time I'm testing a work around by backing up a 'lastexit.sim' file for each of my instances. Maybe when that file gets overwritten it doesn't get COMPLETELY overwritten, so data from more than one sim ends up in it. Just my theory though.