You can use the Export functionality to Export the configuration and Import it into a new environment, assuming it is the same version (not sure if it works across support packs, e.g. exporting 5.0 SP2 and importing into 5.0 SP4).  

I've exported an AG appliance configuration before and imported it into an AG service setup, so I know that works (just gotta fix all the IP address assignments afterward).

Another option would be to add a secondary admin console, destroy the old primary, and promote the secondary to primary.  That is a more complex process, but I've done that before too when moving from SuSE to RHEL.  Then you can just build new IdP's and AG's and add them to the system and remove the old ones.

And of course, the manual option is there too.

So lots of options.

Matt