Multiple copies of same document shown in iTunes

All my documents are in a folder My Documents/iPad.  This contains Epub and PDF documents that are read by iBooks reader on my iPad2.  When I go into iTunes select the iPad and then ask to look at the books is shows these books/PDFs in the folder.  That is if I have added them to iTunes using the Add file option.  They then appear with a Tick Box.  If I tick the box and say Apply, they appear on the iPad and iBooks can read them.  However I now have these documents in iTunes shown multiple times. So a documents say Fred.PDF is shown 2 times and in somecase in 3 times!!  I can't see any way to tell iTunes to remove these documents from its record of what it believes there is.  You can Add Files to iTunes but I can't a DELETE.  I can't see anyway to delete these files from iTunes record/database?  One might want to delete Ebooks or PDFs otherwise this database/what is shown under books in iTunes would grow and grow with no way of cleaning it up.

I'm having the same problem. Numerous copies of many apps in itunes but not on my iphone. I also have a problem with itunes showing that I have 5 apps available for update but they never change. The iphone seems up to date but those 5 apps still show as pending update in itunes. Today it showed 8 updates available but after all was done the same 5 remained. When downloading all 8 seem to be downloading but after it finished I still have the "5" apps listed as needing to be updated? Very frustrating.

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