In SAP Standard Employee master data replication from SF EC to SAP HCM using report ECPAO_EE_ORG_REPL_QUERY we have an option to filter employees based on company code or country or Employee Class while sending query to SF EC as shown below,

Query Parameters
But if there is a requirement to filter replication based on PERNR and USER_ID. Find below the approach.
Create a Custom Table ZHR_EMP_REP_FLTR like below.

Table: ZHR_EMP_REP_FLTR
Create a maintenance view ZHR_EMP_REP_FLTV as shown below.

Maintenance view : ZHR_EMP_REP_FLTV fields info

Maintenance view: ZHR_EMP_REP_FLTV Status info
Generate a Table maintenance Dialog with no recording routine as below.

Table Maintenance Dialog : ZHR_EMP_REP_FLTR
Create a Transaction code for maintaining the Entries in the Filter table as below.

Transaction code : ZHR_EE_FLTR
Now assign above Transaction code ZHR_EE_FLTR to Master data team as per need.
Master data team will enter employees info needs to filter as part of Employee master data replication in above view using transaction ZHR_EE_FLTR.
We need to create an implicit enhancement ZENH_FILTER_PERNRS in method GET_BASIC_PERNR_DATA_TAB of SAP standard Class CL_ECPAO_IN_PERNR_OF_EMPLOYEE to do actual employee filter.

Enhancement ZENH_FILTER_PERNRS
Filter employee and Populate a message in the code as below to pass info back to SF EC Data replication monitor as below.

Code to Filter and Populate message
SLG1 Sample log looks like below.

SLG1 Sample log
So in this way we can exclude employees from replication to SAP HCM as per business need in Core hybrid scenario..