I would keep the original file from which the run time copy was generated. That file's design will be identical to the runtime file, but it will still have the .fmp12 file extension so you can easily open and update the design should that be necessary.
You should also be able to open and edit a copy of the runtime file as well, you'd have to open it from the File menu instead of double clicking the file and I don't know if you'd have to change the file extension back to .fmp12 first or not.
This page goes into more detail than most
Did FileMaker just open the door for developers to create
databases that will run on Macs, Windows, iPhones and iPads, all for free?
Knowing that several of my clients will need more than one runtime (in come cases multiple bindings of the same solution with different file extensions to be used for multiple entities), I wondered if running the runtime file in iOS with a custom file extension would work. I just tested it with a prefix other than .fmp12 for both the Mac & PC platform runtimes and an iPad and both worked. The icon is not the standard FileMaker one (and they show up as "Other Documents" in the FM Go App files on device listing) b/c of the different file extension, but the program still worked & changes to the data were saved! PhilModJunk, I noticed that you suggested that the file extension might need to be .fmp12, so I am not sure if there is something I am missing in my test, and if so, would you mind filling me in please? Thank you!