Hi Jay,
It's been a long time, so you would have resolved this already.
However, for all others, the reason for duplicate employees is due to improper locking when executing the work processes for the IDocs in CRM post the HR data.
In order to avoid this, in CRM, in the Partner Profiles for the sending system (ECC), (WE20) ensure that for the Inbound parameters (HRMD_ABA), the "Processing by Function Module" is set "Trigger by Background Program".
This will avoid the locking issues and causing creation of duplicate employees.
Now, when you change the process from "Trigger Immediately" to using the Background Program, all new IDocs from ECC-HR will be set to status 64 in CRM.
In CRM now, setup a background Job for Program - RBDAPP01 to pick up any IDocs of type - HRMD_ABA in CRM for status 64. This program will post the IDoc.
FYI, in our scenario, we setup RBDMIDOC in ECC to post the IDocs every 10 minutes, which get processed in CRM by RBDAPP01, also, every 10 minutes.
Regards,
Nelson