ITunes' "Sync Apps" and iPad do not match.

Trying to figure out what my options are here (and what might have happened to cause this)...
Currently, the "Sync Apps" box under the Apps tab in iTunes is unchecked. The image displayed of the iPad reflects the correct number and placement of apps on my iPad.
Checking "Sync Apps" changed to a much-reduced set of apps, with placement that is WAY off.
While I'm interested in what might have caused this, what I'm more interested in is figuring out how to get the two in sync. I can't run the risk of losing data on the iPad and, if possible, I'd prefer not to select apps one-by-one in iTunes (there are about 100 I need to sync). Any thoughts?

Please, show this:
- https://discussions.apple.com/thread/6037934
- https://discussions.apple.com/thread/5943168?tstart=0

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    iTunesMobileDevice.dll!5d2efcb7()
    Unknown
    iTunesMobileDevice.dll!5d2ebc94()
    Unknown
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    Unknown
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