Assuming that you are using Continuous CMDB Sync, the data will be inserted into the new CMDB dataset as your Discovery jobs are executed. ADDM will find that the data does not exist, and it will insert the data.
I recommend these steps to switch over to the new CMDB:
1) stop discovery runs (you could put the appliance into maintenance mode)
2) stop continuous sync (wait for it to finish processing its queue)
3) change configuration to the new CMDB dataset
4) test the connection to the new CMDB dataset
5) test by sending a couple of hosts to CMDB
6) start continuous sync
7) take appliance out of maintenance mode / start discovery runs again, etc
I added the section, "Preparing synchronization to more than one CMDB" to the documentation that details the steps that Lisa provided in her reply. If you find any issues with the process on your end, please let me know and I will update the documentation as necessary.