It is not unusual to transfer responsibilities between University partners in projects – it is usually as a result of the head researcher moving from institution to another.
The “standard” practice seems to be for the “first” partner who starts the work to report the costs on his form C (sometimes with special period, where “first partner” actually leaves the project as a result of the transfer) and the new partner to report his costs on subsequent form C’s.
The budget distribution between partners (and therefore funding) needs approval of all partners and the project officer of EU, but this is probably a formality if there are no time slippages and quality of work results is maintained.
In our opinion there should therefore be no accounting/invoicing between the two institutions – the accounting for the changing in funding is via the consortium. If first partner needs to refund over-funding he does it via coordinator or under coordinators instructions.
The changes and work done by first and replacement partner need to be reported on the periodic activity (technical) report (indicating that it has been done with consortium and PO agreement) with reasoning for the change indicated.