So... VISRETAIN is it?
You know, I think I've used VISRETAIN... maybe 2 times in my life.
See what happens when you get stuck in the one-way mindset?
that's it, and if you have a later version of the software than my "unpatched" first release of R2002, you just turn off visretain, and hit RELOAD in the xref manager.
If you always want the xref to show the layer settings from the original, just leave VISRETAIN off always.