immi101: yes, you can disable it you lose a bit convenience, but on the other hand you don't have to deal with removing orphaned menu entries when not uninstalling things properly. Now uninstalling means, just delete the prefix folder and you're done.
don't know the exact extend of PoL abilities, as I don't use it myself ( I prefer the greater flexibility of the terminal :) )
But I see lots of people using it as a simple GUI to start their programs who are happy with it.
So at least it seems worth giving it a try.
don't have any experience with xfce. maybe Whisker is more picky about parsing the .desktop file (or it has a bug).
got any spaces or other non-ascii characters in the Exec= or Path= entry?
Hmm, nice; I may end up scripting and using that if I get sick of trying to fix this.
See, that's the weird thing. I do have spaces in them, but Worms Armageddon works whilst Europa Universalis III does not, and their .desktop files are identical (except the game names of course). Since they all work when run directly but not through Whisker menu, it must have something to do with it...
clarry: Wine setting up a new prefix in ~/.wine-whatever (assuming this is your old prefix) means one of these files still contains instructions for wine to do so. Find that file and fix it. I'd start by grepping for wine-whatever under ~/Desktop and ~/.local. This question isn't so much about moving prefixes as it is about fixing desktop files or whatever...
For anyone constantly renaming directories or considering mounts, maybe you could consider a simple script instead? I hacked one for myself in five minutes back when I realized it really is better to just install everything in its own prefix. Disclaimer: might not work for you, no warranty. I never use spaces in filenames ;-)
http://paste.dy.fi/SCe/plain I have stored as ~/bin/wp, chmod +x, $HOME/bin in $PATH.
The idea is to automatically create (if not done before) and switch into a prefix without polluting your old environment. To do that, it runs a new shell which sources your normal bashrc and sets a few extra things, including a prompt to remind you that you've set a wineprefix. Exit the shell normally and you're back in the old clean environment.
grep isn't showing anything of interest, but maybe I've fixed that, I dunno. I'm getting myself confused now as to what I have and haven't done, and it may be best to just wipe my hands of all this and reinstall the broken prefixes or abandon the .desktop files entirely; we'll see.
That script is nice, I may co-opt it :)