If you restart nios2configtool and supply your updated PTF file on the command line, then reopen your saved project - that should do the trick for you.
To be on the safe side, I'd recommend you also delete your install directory, and then regenerate it by selecting:
Build->Generate Build Tree
Build->Library
in configtool. This will make sure you flush out any old configuration data.
If you want to keep your existing project, and start a new one for the new hardware, then just copy your old .ecc file to a new location and open that. You should then run:
Build->Generate Build Tree
Build->Library
as before.
The only values that won't update automatically are those that you have previously edited manually. For example if you have changed your .text section to be in a memory section other than the default, then it will continue to be in that section (even if it no longer exists), so you may need to fix things like that up by hand. If this is required than you should get an apropriate configuration error to warn you.