If you backup the ipad 1, you'll probably get a message stating that there are apps that are not part of the current itunes library.
I beleive it will delete the ones that are not part of the library you are signed in with.
You should try to backup first anyway.
At any rate, you can always re-download any content directly to your ipad or compouter by signing into the itunes and app stores, and then going to 'purchased'.
About iOS backups
iTunes: Backing up and Restoring iOS software