Suggestions on managing chartfields and combinations for T&L and Payroll processing

We currently use chartfield SYNC messages and COMB_EDIT_CF_REQUEST / RESPONSE in order to validate combination data when a user enters it on timesheets and when we use it in payroll for pay lines or in expense mapping configuration. We have an absolute ton of chartfield values, but it has come up a few times now that my payroll managers would like us to be able to limit use of certain chartfields and combo codes. For example, we have over 1000 department ids that are valid and active in Financials, but none of them should ever be used in HCM. The problem is that with the delivered combo messaging if it's valid in FIN it's valid in HCM. The documentation on the combination code setup is really confusing to understand as well. What are your suggestions on how to manage them?