Reference drawing layers can be modified in the parent drawing and changes to color, linetype, and other properties are maintained as long as the system variable Visretain is set to 1. If you want to restore the layer properties from the child drawings, you can set Visretain to 0 and reload the reference. If you forget about Visretain, however, you could lose the layer settings later on.
This routine from Benzigar Peter allows you to reload an xref while restoring the original layer properties, and not have to worry about the Visretain settings. After you load the LISP file, run the command Xrecol and select the xref. The LISP code sets Visretain to 0, reloads the xref, then sets Visretain back to 1.