Oh that happened to me when I moved houses and had them stored that way!
I have had that happen to me several times. I finaly gave up on seperating them one day. I just decided that it would be a new mix for an eyeglass chain or too.
I love seed beads and intermingle them with other beads all the time. This happens to me a lot (when small dog decides he must be in my lap when I am doing some free form netting work!!) and I just keep a SOUP jar and leave it at that. When they mix they sTay mixed and sometimes I find the Mix is the perfect thing for my project!!!