Hi @IMS,
Thank you for posting in Intel community forum, hope this message find you well and apologies for the delayed in response.
Clarification if I may, situation here is that we have a set of different NIOS with different flash, and you are trying to copy the application of both NIOS into the shared on-chip RAM to run it yes?
And only one of the NIOS application are successfully working?
If that is the case I would recommend the following tutorial here, as it would be a very good starting point for a multiple processor system.
Warm regards.
BB