Cyclone V flash upgrade problem

What configuration scheme are you using? Is the Atmel part you mention a micro that configures the FPGA or a memory part that the FPGA configures from?

If the former then you need to solve this in the micro.

If it's a memory part then read through the 'remote system upgrades (https://documentation.altera.com/#/00005773-aa$nt00073227)' section of the Cyclone V Device Handbook. The altera_remote_update megafunction comes in handy here. Look at the "altera remote update ip core user guide (https://www.altera.com/en_us/pdfs/literature/ug/ug_altremote.pdf)" and, in particular, the design examples.

Cheers,

Alex