Hi Ajeesh,
Program RFCHKU00 executed in tcode FCHU is using FM (function module) DOCUMENT_CHANGE to do the changes in fields Reference (BPKF-XBLNR), Assignment (BSEG-ZUONR) and Reference3 (BSEG-XREF3). Unfortunately, this fm does not trigger FI substitution (OBBH), so you won't be able to change any fields via substitution when executing FCHU.
You have at least 3 alternatives:
1) Try substitution in another transaction (eg. when posting, etc)
2) Try BTE or BADI to change the document (triggered in FCHU or payment, etc)
3) Copy program RFCHKU00 to a custom one and follow what is said in the code:
* -> If a further field of the document is to be filled with *
* the check number, additional lines, which correspond *
* with ** (double star) characterized lines, must are inserted. *
See comments in the source code beginning with **
Best Regards!
PS: in table-field PAYR-ICREF is being stored which option was choose in FCHU to update payment document.