> 
> On Qubes xfce 3.2 I had the entries in ~/.local/share/applications
> and the directories in ~/.local/share/desktop-directories
> 
> not sure if it is the right place to clean up however...

It worked for me.
Got rid of the old fedora-23 and debian-8 listings by doing as suggested above. 
 ie. going to  ~/.local/share/applications  and doing  rm -fr <each entry for 
the vm to be removed>  
 Once each listing for,eg. fedora-23 was removed then fedora-23 disappeared 
from the drop-down.
  Could probably have done it quicker via ~/.local/share/desktop-directories 
though?
Thanks for the advice @Tom Zander and @dy...@riseup.net

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