iTunes saga 5.0.1
iTunes is not a device management tool
It is a media management tool. It was made to put music and videos to iPod which started as an MP3 player. Some say it sucks there as well. I don't care. I copy photos as files, I transfer music with MediaMonkey and use mail and Dropbox to manage documents.
iTunes is patched to be a device management tool with key functions obscured by the media-optimized interface.
One of the most scary checkboxes in the Apple universe is the "Sync Apps". User is warned that if selected, all apps installed by the user on device will be removed. And they are. The trick is that before one does that, it makes sense to "transfer purchases". So that after "sync apps" removes them all, you can put them back. They get rearranged on the springboard pages but after a few minutes' work things are back to normal. It seems. It is still scary!
What sync should do to justify its name is to really sync - compare content on the device with content in iTunes and allow for both to be the same after the process. Actually I see no point in syncing stuff - apps are installed via WiFi anyway and purchases remembered by the AppStore in case one deletes them by mistake. But I decided to sync, because:
Before upgrading to iOS 5.0.1 I backed up the iPad. Upgraded. But when I restored it, there were no apps installed, just some 5 GB of memory was occupied with "other". Some backup! I would expect a backup to backup the device. Perhaps Apple would care to offer a selection of what to back up. Like system settings, apps, apps' settings, apps' data, music, videos ... But no. It seems only the things are backed up that are synced!
So I installed the iPad from scratch. Which is not a bad idea every now and then. Get rid of all the junk and dead wood and start clean.