If you are planning to remove have the SEPM on the same server and just to change the database type, follow the disaster recovery process (which is nothing but database backup and restore and then restoring the recovery information). (Note: backup and restore can be done between SEPM with different types of databases). While following this method there will be a short time of SEPM unavailablity.
If you are planning to install a new SEPM on a new server, install the new SEPM (with SQL database) as the replication partner of the existing SEPM and then move the client over to the new SEPM by reconfiguring the MSL and then decommission the old SEPM (with embedded database).