A shared custom Instruction between Nios II processors

So as dsl mentioned, you really need to have one instance per CPU or you need to do more work.

Qsys, unfortunately, will allow you connect both NIOS Custom Instruction Master ports to your single Custom Instruction Slave port, but when it generates the system you will find that only one of them actually got connected.

This type of sharing is probably better suited to an Avalon-MM Slave style IP where Qsys will correctly add the automatic arbitration logic for you.

Or if you wish, you could probably add the Custom Instruction arbitration logic yourself: either create a new IP block with (2) CI Slave and (1) CI Master connected to your current IP; or alternatively you could simply add a second CI Slave port to your existing IP block and perform the arbitration internally.