Backing up iPad apps purchased with two accounts?

For a recent sync, I "transferred purchases" from my iPad to iTunes and subsequently synced it to my iMac with my personal AppleID. Before syncing, my iPad had apps purchased with two separate AppleIDs on it.
Upon doing a restore for the iOS5 upgrade, the apps purchase on the other AppleID account don't show up on my iPad.
Where are the apps now and how can I get them, and their data, back?!? I know I can log into the other AppleID on my iPad and redownload the lost apps from the App Store. However, I need the DATA from the apps (note taking apps and such). How do I get that data back?
If this isn't an option, this is a major fault of Apple's account design.
Thanks in advance for your help and suggestions~

Hello J_DougBC,
Thank you for posting in the Apple Support Communities. I found an article that addresses Apple IDs that are different than the Primary Email Address on the account. You will need to go to https://appleid.apple.com/ to "Make your Apple ID and email address one and the same."
If your Apple ID and primary email address do not match, or they match but the email address is unverified, you can edit them.
1. Sign in to My Apple ID to manage your account information.
2. If you want to add and verify an email address that matches your Apple ID, follow the dialog box that says "Make your Apple ID and email address one and the same." This will automatically unverify that email address from any other Apple ID for which it was previously verified.
3. If you want to change your email address to one that does not match your Apple ID, click Edit next to your Primary Email Address. If this email address is already associated with another Apple ID, you will need to sign in with that Apple ID and delete it before you can add it to your preferred Apple ID.
Note: If you have an @me.com or @mac.com Apple ID and primary email address, you cannot edit your primary email address once it has been verified. To change your @me.com or @mac.com primary email address to another email address, contact Apple Support for assistance.
You can find the full article here:
Associating and verifying email addresses with your Apple ID
http://support.apple.com/kb/HE68
I hope this helps get you back on track!
Best,
Sheila M.

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