Upgrading the SEE server results into creation of another IIS Site which is appended by numbers and this services are turned off.
SEE 11.4 MPx, SEE12.0 , SEE 12.0.1
Once you upgrade the SEE server, its a normal behavior for another site to get added for the newer version and the older version gets appended by numbers where its services are turned off.
Example: Symantec Endpoint Encryption Services_XXXXXXXXXXX.
After upgrading the SEE server then it creates a stale/old entry in the IIS site which is appended by numbers and this stale entry can be deleted safely.
Recommended best practice: Take a VMsnapshot backup and database backup for any disaster recovery.