Content deleted from bin-debug on launch

In Flex Builder 3 in a project part of the content, which is copied from the src directory to the bin-debug directory, is removed after launching the project. When I clean the project all data (swf files etc.) are copied to the correct locations in bin-debug, but after I change any single line of code Flex Builder removes all files from bin-debug and only partially copies the files from the src directory. Behaviour isn't consistent, sometimes folders are partially copied, sometimes nothing from a folder is copied.
What could this be?

I figured it out a sollution it is quite simple.
1) Connect your iPad to the computer and go to iTunes.
2) Select your iPad from the devices list
3) Select the iTunes U tab at the top of the screen.
4) Make sure you have Sync iTunes U checked
5) Make sure you are automatically syncing the files you want.
Personally, I only do one course at a time and want all the videos for that course.  I prefer to include all the files of a selected course, but you could use any settings.  I think the default is to include all unplayed items for all courses.
AFter verifying the above, it should not delete your videos on sync because it will actually sync them.
I figured this out after one of my video downloads stalled and I was told that the videos are actually managed by iTunes, not iTunes U.  I hope this solves the problem because it solved mine.

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