Why did iTunes delete 2000 photos during Sync, even with 1 GB free space

I am having real headaches with Sync function in iPhone/iTunes. The 2 biggest problems concern Contacts and Photos.
Photos: I used to have 4465 photos on my iPhone, using 1.47 GB at a time when my iPhone still had 0.67 GB free capacity out of its 29.3 GB total. About a week ago, while syncing with iTunes, I saw the error message on my PC stating that there is not enough space on my iPhone to copy all photos. At the end of that sync, I was left with only 2072 photos using 0.78 GB, while the free capacity on my iPhone increased to 1.6 GB. I have synced at least 10 times since then to try and recover my photos, I have deleted the 2.4 GB photo cache, but exactly the same error message and issues happen. Please help get my photos back into my iPhone!!?
Contacts: my iPhone is the principal device on which I put new contacts or update existing ones. After syncing, sometimes I see that the new information entered into my iPhone is no longer there. And so I lose contact with people, since I have no other records! That’s really frustrating.
I have tried upgrading my iPhone software from current v4.02 to the latest v4.1, but for the 5 times that I have tried my WiFi has timed out, and so still not upgrade, as Murphy Law would have it!

I guess I should have included a little more info:
1. I only have 1 appleID
2. I only have 1 apple device (the one iphone, nothing else)
3. I only sync on one computer (VERY annoying you cant use more than 1!!)
4. I never have any other problems during syncing and don't change any settings
5. I downloaded the app again so it is back.
I am not asking how to get the app back, I just want to know WHY itunes deleted this app. This is the second or 3rd time it has happened and it is really annoying.
I also would like to get my files back. So again, I'd like to know why itunes deleted the app and if it deleted my files as well.
The most important part of this is to find out WHY this happened so that it wont happen again. It seems to be a pretty simple operation: Plug the iphone in, itunes opens and does a sync. It almost always works perfectly, I never change any settings. Yet every once in a while it deletes a newly installed app so obviously something is wrong. If I can find out what I did wrong, then I can avoid it in the future.
Thanks!
Scott

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