I have had any problems with some URI in the database, that was because a development site on a subdomain got into database somehow. Now I substituted the wrong links witht the right links on a fresh export with an editor and would drop all tables and re-import the corrected DB. Would this procedure involve any problems with BPS?
I followed every step exactly (on a second try I also deleted wp-admin and wp-plugin htaccess), then loaded the database up, that only had 130 URI changes (links to images were wrong) and then it wont let me in admin panel anymore.
Yes, in your case you are changing database content and not doing a straight clone or migration so yes you would have to change your database content for the new site. I should have stated that the Migration/Clone link above is for making any exact copy of the site.