How to Override Company and Cost Center for FI Posting from HR Payroll

Question

Current problem:  A company code has been 'merged' into another one and the old company code can no longer be used.  In the last payroll run, there was a rate change that caused a retro back to the time of the old company code and since the old company code and cost center were closed, the FI posting error'ed out.  To correct, we had to delete the offending pernr from the cluster and back out the rate change until we came up with a solution. 
Investigation has revealed a process called 'Substitute Cost Centers', but we tested it and a 'flusher' cost center is required to be set up in the old company code and FI refuses to open it up. 
Also, I've located 3 user exits for RPCIPE00, but I do not see where  company and cost center can be changed.  So I've tried to code my own BAdi, but there seems to be a header company code that I'm not getting.  The item company code and cost center seem to be doable, but I don't know how to change the header company code.
I am new to HR and Payroll having spent the last couple of years in BI and before that I worked with the material master and Purchasing.  It is my humble opinion that the company should not have been 'turned off' until Payroll was finished with it and that means 2 years until we archive.  In reading about symbolic accounts, several times it is written not ever to delete them.  Seems to me company code is the same.  But surely I must be wrong and there is a solution that will make everybody happy. 
I would appreciate any and all ideas.  Thank you so much.

Answer 1

Amosha, thank you for your response.  Here is PCP0 that shows what I mean by 'header company code' that I don't see how to change (I re-ran pd 26 2008--bi-weekly payroll, btw):
06/30/2009 Posting Document
Run                      0000002791
Company Code    0057
Document            0000008174
PostingCurrency  USD
Reference           HRPAY00009
Doc. Type            ZB
Run Type             PP
Posting Date        12/01/2008
Documant Type   G/L Account Document   
Document Date    06/30/2009
Bus. Transaction HRP1
    There are error messages for this document
Account Number with Text
21301000   Accrued Salaries & Wages   CCTR 14515      ...
20303998   HR P/R Doc Split                                               ...
Messages for Document 000008174
Error in document: HRPAY 0000008174
The CO account assignment object belongs to company code 0001, not 0057
Company code 0057 is now closed and has been merged into 0001.  Cost center 14515 in the above doc was populated by my clone of RPCIPE00 and call to my BAdI which retrieved current company and cost center from PA0001.  You can see from above that the 'header' data still shows 0057 and indeed, my version of RPCIPE00 only changes P_ITEM-BUKRS, P_ITEM-KOSTL and P_ITEM-SGTXT.  It looks to me that fm HRPP_TRANSLATE_FICO gets the 'header' company code afresh.  I was planning to leave WPBP-BUKRS (and all other Payroll data) alone (ie, not override company code).
As for your other question, we post retros to /551 and /552. 
Thanks again.