ITunes deleted all the Applications from the iPhone...

Question

I just plugged in my iPhone to charge the battery and as it began to Sync, I saw it was deleting applications.
At first I thought this was happening as a part of updating a couple of the apps, but as I watched it begin to delete them all, I switched to the Applications tab and saw that while "Selected Applications" was checked, none of the Applications themselves were.
Then iTunes began telling me it couldn't sync because "the disk couldn't be found" or something like that. After a few attempts, I turned the phone off and on.
In iTunes I selected the apps I wanted on the phone and then plugged it back in. I started the syncing process and the apps began copying to the phone.
BUT, when I checked the Applications tab, I noticed it had reverted to my previous list of selected Apps. Now I get to perform the unpleasant task of trying to rearrange them the way I had them. Fortunately I make screenshots of each page when I make changes, but moving them between pages and getting them to settle in where you want them is a pain the butt.
I don't know what caused this to happen, but it's unnerving.

Answer 1

A bit of a similar story.
Bought a new MBP, and transferred everything from the old MB to it. The migration process is just amazing, at least it seemed so.
Due to limited disc size in MB, I had iTunes library on an AirDisc. The setup was a constant pain in the butt, since iTunes seems to be faster than the waking up of the sleeping connection, leading constantly to "lost" songs. One of the reasons for buying the MBP was to have the iTunes library (of about 90GB) on its disc.
The migration did not transfer the library of course and I did it manually by connecting a USB cable, configuring iTunes music folder pointing to MBP and consolidating library. I have no idea why, but it took three attempts to finally succeed, I eventually had to erase all songs from iTunes and then choose "Add to Library" pointing to the disc as a whole.
Everything looked cool, except of course empty playlists. Connected the first iPhone, and got a message asking if I want to transfer purchased apps from the phone to iTunes. In case on answering "NO" they would be erased from the iPhone. Obviously I chose the transfer. To my amazement, iTunes started to promptly erase apps. As some others here, I thought it is part of the process. After the sync I noticed that apps were really erased from the phone.
Came here and did the logoff-logon, unauthorize-authorize trick, hooked the other iPhone the the MBP and after the same dialogue as above, this time iTunes did copy apps back to the computer.
Synced the first iPhone, and everything came back to normal.
Without the second iPhone, I do not know what I would have done.
Obviously, when changing to a new computer, you should authorize it BEFORE the first sync.