Hi,
as the EP2C20 used on the board should be the 484Pin package supporting vertical migration as shown in the handbook your idea should be generally feasible. You should check nevertheless for differences in Pinout between the EP2C20 and EP2C50 and for the configuration interface on the dev-board accepting the larger config file for the EP2C50.
Last but not least you should check for a company to replace the chip physically - as there is some distance between the FPGA and other devices required for the desolder / solder process...
To cut a long story short: It should be possible but to be 100% sure some stuff must be checked first...