Cyclone 3 does not configure

Yes, it's a pain when hand working the boards. What we do is either solder paste it, and heat the bare board up on a hotplate with just the fpga until the paste flows, or pre tinning the board pad, then the chip pad and doing the same trick with the hotplate and a hot air gun until it flows.

Works ok with lead solder but is a royal pain with ROHS solder. (Much more likely to thermally damage the part)

Another option I guess would be to use an electrically conductive epoxy like http://www.mgchemicals.com/products/adhesives/electrically-conductive/silver-conductive-epoxy-8331/.

(Although I haven't tried that)

Note: Arctic Silver 5 won't work. It's thermally conductive but not electrically conductive even though it has "Silver" in the name.

Pete