Frank,
Do NOT run delete or truncate commands like this on the NFA 9.3.5 and up Harvester database. Due to the way the database has changed, using MySQL queries to delete routers and interfaces will corrupt the database.
As far as NFA 9.3.3 and earlier, deleting routers and interfaces like this from the Harvester database shouldn't be a problem. The router/interface information should repopulate when you receive netflow without affecting any of the existing data. We don't like to encourage this because of the danger in general of making a mistake, so if you choose to manually delete routers in NFA 9.3.3 and earlier make sure you have good backups of ALL your MySQL databases.
For example, I've seen customer's attempt to truncate the 9.3.3 harvester.routers table (OK), but accidentally truncate the reporter.routers table (Not OK).