That strikes me as odd, but OK, I believe it.
Well all I can say is that I would have synchronized the iPad with its main computer and updated all software through that to begin with. I don't want to just say 'user error' but it seems you are using things in ways which seem pretty unorthodox and non-intuitive (to most people). Initiating a manual backup on one machine, but no synchronization, and then doing what you did on another machine? This is why I'm having trouble following the links to see at which point your data got lost and where you could turn to get it back. Others have given some answers to tat I believe. I agree that it is frustrating and that software should be as simple as possible, but at the same time, no matter how simple a tool is, there's always the wrong end of the knife to hold, if you know what I mean.
Good input.
Let me try to clear things up with a more detailed breakdown. This is the best I can recollect.
Machine 1
1. A few weeks ago I was going to try to exchange my iPad 2 for a different model, so I connected it to my laptop (PC - Windows 7), and made a backup.
2. I then did a restore (*not* form backup) on the iPad to completely wipe it of all data and restore it to factory settings.
3. I learned that iPad 2 is perpetually sold out, and so decide to stick with the model I originally bought.
4. I restored the backup I made, and everything was peachy.
---
This is the last time my iPad was ever connected to machine 1. For two weeks I used my iPad without connecting it to a computer.
---
Machine 2
1. Last night I decided to copy the apps I had accumulated on my iPad to my home PC, as well as make a backup.
2. I opened iTunes and connected my iPad and it was recognized correctly.
3. It prompted me to do a software update. I clicked cancel.
4. I right clicked on the iPad in iTunes and selected the "Transfer Purchases" menu option, which copied my apps to my PC.
5. I went to the apps tab in iTunes and checked sync apps, hoping that it would allow me to keep my applications, since they were just transferred to the PC. Unfortunately, it prompted me with a message that said all apps would be deleted. I clicked yes, to see if what I've read on the internet about it not actually deleting the apps if they have been transfered to the pc was true. This was not true. All apps were deleted.
Design Aside: I didn't care *that* much that the apps were deleted, since I had just made a backup of my data. But for me, this is poor design choice #1. If an iDevice is able to transfer it's purchased apps to a computer, then it should be allowed to keep those apps installed. Both the PC and my iPad are registered to the same iTunes account. This is something Apple could and should, in my opinion, change.
6. I initiated a software update on the iPad.
7. As soon as the update completed, it automatically created a backup which overwrote the backup that I had created manually.
8. When I went to the restore options, only one iPad backup was listed, and restoring to it did not restore my original, pre-app deleted state. My data was gone.
Design Aside: This is poor design choice #2, and the worst one of the two. Right before Windows installs updates, it creates system restore points. Once the update completes, it doesn't overwrite that same restore point with a new one. That would defeat the purpose of creating that first restore point. It is my opinion that Apple should never overwrite a backup, unless the user is prompted first. That would be a good design. If they want to keep messages out of the users' faces, then they could compare different backups and delete the smaller one. There are many more intelligent way to handle backups that don't involve simply overwriting manually generated ones. This was most disappointing for me to experience, not just because I lost all my data, but because I like how Apple designs most of their products, and cannot understand why they would be so shortsighted when it comes to something so critical.
Anyway, it's over and done with, and my lesson is learned. I can't trust the backup process without copying the backup folder outside of the MobileSync directory, which is really too bad, because I'd like to be able to rely on iTunes to manage the backups for me.
If anyone would like more info about a specific thing missing from the above description, just let me know.