>the certificates are now working on the Windows box the same way as the Linux box
Good!
>If I dump those records and then move them over to the Windows box to make everything current will it overwrite all the current records
mysqldump takes a backup of ALL the records.
mysqldump –uUSR –pPWD –K –E –A –R –f >some_backup_dir/mybackup.sql will dump ALL of your current server into a file that can be loaded into your new server, as you have already done.
If you dump and load again, you will effectively remove everything from your windows database, and copy the linux database to it again.
IOW, you can't just dump and copy new records. You get the lot.
If you want to maintain both databases into the future, you could use replication and have say the linux machine as MASTER and the windows as SLAVE.
This has the limitation that all writes to your database MUST go to the master, but you can read from either.
http://dev.mysql.com/doc/refman/5.0/en/replication.html
There is also possibility of both being MASTER and SLAVE to each other, but that can be tricky to set up and is not for the feint hearted.
Good luck,
Barry.