I purchased some apps in Argentina store, and then I moved to US store, and also got some apps.
Now I'm no able to automatically update the apps I got on Argentina store.
I tried to delete all my apps and re-download them at the US store, but that didn't work.
For example: I tried to download Skype for iPad in the US store, which is free, and it downloads it, but keeps showing as "Free" instead of "Downloaded", therefore I am not able to update it in iTunes with the other US apps.
Best Answer
I learned that unfortunately the best solution when moving to another country is to open a new account in the new country and go through the tedious task of logging with different accounts when you do the updates.
I didn't do that but my wife did. And now I have the exact same issues plaguing my account as you do. I moved from North America to Europe.
I partially solved the problem by restoring the iPhone and iPad. deleting and re-downloading the apps in iTunes and re-syncing the iPhone and iPad.
Now most applications simply appear in the Apps "Updates Available" section. Otherwise they can be updated directly from the iPad or the iPhone then synced back to iTunes.
But next to my Apps I still have 27 apps as showing for updates but I can't download them as the updates are available in the US store and the apps have different versions in the US than in my current store.