IOS upgrade forced an Apple ID change. Now my Apps are Broken!

Hi all, after 25 years of using macs I've finally encountered something that isn't intuitive!
I have had the same Apple ID for about 7 or 8 years, however when I upgraded my iPhone to ios5 a couple of months ago I could not get past the upgrade process because my Apple ID was being rejected. All my other Macs and iPad were still logged in to the iTunes Store so I couldn't understand why. However it looks like iOS5 requires the User Name to now be an email address. I could no longer use my perfectly functioning existing User Name, and instead had to change it to be my email address, which I did online with the account management function of the Apple Website.
However now it appears that my previous Apps are no longer considered part of my account. I've just bought a new iPad and wish to migrate my old iPad, account and Apps to it, however most of my Apps are not listed if I attempt to 'sync' Apps. How can I get it all to unify again? thanks!

To answer my own question, to get around the problem I didn't auto-sync my Apps in the end! I just manually selected the ones I wanted and tried to duplicate what I had on my old iPad. A bit hit-and-miss and very time consuming, as I had my iPad set up in a very particular way. It's a shame because migration assistant on my macs allows me to clone every last setting to my new macs - docs, apps, system, desktop, the lot. Why can't the iPad be the same!

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