Cyclone and Cyclone II compability

Basically, you have to create a pin assignment for the new chip. To check, if the design fits the new chip at all, you may want to remove all of the project's location assignments (it's done automatically when chnging the device) and try to compile it. You'll get an overview of resource utilization and achieve timing.

You mentioned EP2C15A, which is only available in 256 pin FBGA package. Don't know, if it's suitable for your assembly technique. It also has less available IO pins than EP1C12Q240. EP3C16 could be used in QFP240 (less IOs than EP1C but more than EP2C) or FBGA256 package.

The VHDL project would be sufficient to check for IO pin requirement, but you should also analyze the schematic for possible issues. Cyclone III needs a (possibly additional) 2.5V supply, but it can be provided by a small SOT23 regulator.