If I understand correctly, an FPGA does not actually have its state "burned in". It effectively boots from the non-volatile memory; the 64 MB Flash memory.
I'm assuming your goal is to be able to switch between compiled programs without all the time it takes to deploy.
My suggestion is to deploy it initially, and then FTP it and copy all the files in the cRIO back to your computer and archive them there, so when you want to switch back to that code, you just unzip it, and rewrite the cRIO's memory with it.
To save time, you could probably even determine which folders hold the code, and just replace those, instead of replacing the OS and everything.
EDIT:
For clarity, I'm going to reference a specific document, because there are three ways of deploying code.
http://decibel.ni.com/content/servle..._Framework.pdf
I believe Barry is referring to "Building and deploying a stand-alone application", not "Deploying the program using the run button" nor "Deploying the program from the Project Explorer window".