FPGA power managment

You mention an EPCS16. Can I assume this is connected in as mode - not AP as you wrote? Configuration time of 250ms suggests AS.

It's a board change but you could use AP configuration - much faster than AS. Look at the AP Configuration section, page 8-21, in the configuration and remote system upgrades in cyclone iv devices (https://www.altera.com/content/dam/altera-www/global/en_us/pdfs/literature/hb/cyclone-iv/cyiv-51008.pdf) section of the handbook. Look at the configuration time equation 8-5 on page 8-30.

You could choose to stop one (or more) clock(s). That will drop the power consumption dramatically. As Kaz say, be careful of your timing.

Cheers,

Alex