Ok, here's your scenario: Xref 'A' into 'B'. Xref 'B' into 'C'. Then when you don't want to see 'A' you just unload 'A' in 'C'.
Here is a workaround (although cumbersome): Xref 'A' into 'B' and 'B' into 'C'. When you don't want 'A' in 'C' open 'B' and change xreftype (just double-click type in the xref manager) to "overlay' for 'A'. Then save 'B' and reload 'B' in 'C'.
Easy right? Not really but it is a workaround.
Hope this helps,