Is cyclone II reconfigurable?

I cannot answer your question because I have no way of knowing if YOU will be able to do it. (I could not resist!)

I can say that it can be done!

The real item to address and be concerned with is the reload time of the FPGA sub-system.

If your sysem can tolerate the down-time during reload, then you will be fine.

Mission critical components of the design may not be able to tolerate the "missing" FPGA portion of the design.

If you can work within those parameters, then yes, the FPGA will work well for your application.

Keep us all posted of your development.