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Hello. We are on Apps 9.  Would any know if there is a way to apply a customer credit invoice in one company to a customer invoice in another company? Any help would be much appreciated.

I think you are talking about multi-company customer payment…
Yes, it is possible.
E.g. in customer offset window you can select documents from several companies to create an offset. 
System will create intercompany balances (using PP23/PP24 posting types) to balance payment in each company.