You didn’t say how big is your database. Also, if you do this from your computer or if you connect directly to the SQL Server and run the NAV client from there. If your database is a couple of gigs then 12 hours seems excessive, but if it is 750GB maybe not so much. It might be that there is some activity on the database while you are doing the company rename. You have to completely eliminate all traffic while that is going on. I would personally set the database to single user mode before renaming a company.
You can’t take transaction log backups when the database is in simple recovery model by the way, so that part does not seem right.