Hi Rudolf,
In the thread you're referring to the cause was a third party 'system maintenance' app of which one of its features was to automatically delete the settings files and other ancillary files associated with an app if the user deletes it.
In the case of the built-in software update mechanism, Yummy must send itself to the Trash and this third app intercepted it as a user un-installing Yummy, thus removing all its settings and Bookmarks.
I strongly recommend against the use of these so-called 'system maintenance' apps (which I cannot name for legal reasons) because they just cause more trouble and more problems than they actually solve, if they solve anything at all.
So, to the problem at hand:
What's happened is Yummy was 'un-installed' because of such a third party app, and when you then ran the 1.8.9 version it defaulted to the new location of the settings files (Application Support) because the old location (Preferences) did not exist - they were now in the Trash - and so your Bookmarks were 'gone'.
All you need to do is move your settings files/folders back to :
~/Library/Application Support/Yummy FTP
... the new location, and all will be well. Make sure to quit Yummy first, though.
You should move from the Trash (or backup HD) :
DefaultBookmark file
Bookmarks folder
Item Information Database folder
Logs folder
Other Editors folder
Recent Connections folder
Remote Edits folder
Server Favorites folder
All others don't matter.