I recently tested Yojimbo and decided i have no use for this kind of tool, so i thrashed the app and all config files in my ~/Library.
Some weeks later i reinstalled another Mac and set up the .Mac Synchronisation. No problem at all.
I needed my ftp favorites on both machines so i turned to the first to tick the checkbox and saw a broken Yojimbo entry. Not on my mac!
After a little googling i found this tip: Reset the .Mac Sync Server with Syncrospector.
Syncrospector is a little apple tool you can get for free here.
Be careful. The author on macosxhints suggests to reset all sync services which could end up in a total lost of all your contacts. He writes:
Open Syncrospector in the StickiesExample -> Applications folder. Don’t bother trying to use the Unregister button to eliminate any third party client identifiers. I tried “unregistering” Yojimbo’s entry after launching, quitting, and removing the application itself from two of my Macs.
The “Unregister” button in Syncrospector indeed works! The author made one mistake (as did i): he trashed the app before unregistering. To tidy up your sync services with Apples tool, you must not thrash the app in question before but afterwards.
I just downloaded Yojimbo, run it once, unregistered after quitting and than again, moved it to trash and the damaged sync entry was gone.