One month and a few days later...
So it turns out that there is no way to do this to a file added directly in the Deployment project in VS2008 (used to be possible in VS2005...).
But after many many attempts i finally figured out a decent workaround.
I've included the file "Database.sqlite" directly in a windows forms project (Database) with the following properties: "Build Action -> Content file" and "Copy to Output Directory -> Copy always"
Then i added it to the deployment project via Project Output->Database->Content Files
Now apparently everything works fine and the file gets replaced every time i change it and rebuild the deployment project.
This one put up quite a fight ^^
与恶龙缠斗过久,自身亦成为恶龙;凝视深渊过久,深渊将回以凝视…