After updating iPad to iOS 5, iTunes trying to delete my iPhone apps

[JesseA]

Ok, I'm going to try to explain this clearly:

I've had an iPad 2 for a while, and just got my first iPhone (4S).

When I got the iPhone, I plugged it into the computer for the first time and synced some (but not all) of the apps that I already had from the iPad, by checking their icons in the "Apps" screen of iTunes with the iPhone connected.

I've synced my iPhone a few times over wifi with no problem. But today I finally upgraded the iPad 2 to iOS 5. As I expected, the upgrade deleted all my apps from the iPad, but the apps had been stored in iTunes, so I synced the iPad and all the apps were put back, though I had to recreate all the folders and organize the apps again.

Then, after upgrading the iPad to iOS 5, I tried to sync my iPhone again. It warned me that 32 apps would be deleted and asked if I wished to proceed, so I clicked cancel.

I didn't know what was going on, so I clicked the "Apps" tab of my iPhone in iTunes. In the list of apps to be synced (where you can check or uncheck all apps), only the apps that had originally been on my iPad were listed. All of the apps that I had since downloaded to my iPhone were not listed.

Needless to say, I haven't synced the phone because I don't want to lose all these apps. Why is this happening? Why can't I sync a different but overlapping set of apps to the iPad versus the iPhone? Why are some of my iPhone apps not present in iTunes?

I'm using the latest version of iTunes in Windows 7.