Synchronizing deletions between iBooks and iTunes: bug?

Hi everyone,
my iPad2 is configured so to auto-sync all pdfs I have in iTunes.
I delete a pdf on the iPad, then sync with cable.
What I see is that
1) iTunes switches to MANUAL pdf sync
2) it builds up a list of pdfs to sync which (correctly) does not include the deleted items.
But this sounds like a giant bug, because
1) all the books I add to iTunes from that moment on don't get copied;
2) even worse, if I restore auto-sync for all books, then the deleted files reappear on the iPad (I have ~750 math articles...).
Is there a better procedure for deletion?
Otherwise, I'll give up using iBooks and switch to some more serious 3rd party application...

Ratings will only sychronise if you are updating your iPod automatically. If you are managing your songs manually then the iPod and iTunes are by definition not in sync. I have seen Apple Scripts and software for Mac that will sync information, you could try Google to see if anything similar exists for Windows.
For info: iPod 101
The iPod offers three ways to transfer music from your computer. You can select one of the following update modes from the iPod Preferences menu in iTunes (Edit=>Preferences=>'iPod' tab):
1) Automatically update all songs and playlists. This is the default mode, in which your entire music library, including playlists, is automatically synced to your iPod. If the music library on your computer exceeds the iPod storage capacity, you are prompted to select a different update method.
2) Automatically update selected playlists only. With this option, iTunes automatically copies the playlists you have selected to the iPod when you connect it to the computer.
3) Manually manage songs and playlists. You can also choose to transfer music to the iPod manually. This allows you to drag and drop individual songs and playlists from iTunes to the iPod.

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Just curious... the past several months I have noted various concerns around "syncing" between iPhone and iTunes... yet don't recall any mention of whether it occurs between MAC OS or WIN hardware (desktops and or laptops). Furthermore, I am interested if anyone can comment whether these sync issues occurs mostly on TIGER or LEOPARD OS when accessing iTUNES. (Guess I should pay more attention to the noted OS field.
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These discussions include mostly problems, which is what these discussions are for - a user to user support forum for technical support issues and questions.
Which particular issue are you referring to?
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https://itunes.apple.com/us/book/girls-lena-dunhams-twitter/id580909614?mt=11
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Hi Jim - thanks so much for your detailed & helpful reply. I actually do already have those columns shown in my playlist views - my problem is that I don't believe what they are showing!
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Ciao, da un po' di giorni ho un problema di sincronizzazione fra il macbook e l' Iphone 5S. Sul macbook ho Maverik aggiornato e anche il telefono non JB è aggiornato.
Primo problema: la sincronizzazione dura tanto, sopratutto allo step delle applicazioni, rispetto a quando era veloce le applicazioni non sono cambiate.
Secondo problema: la musica, ho flaggato "sincronizza la musica selezionata" ma sono spariti tutti i flag sugli artisti selezionati, ciò nonostante la musica è presente sull' iphone. Ho provato a riselezionarli e me li duplica tutti.
Terzo problema: i libri, succede la stessa della musica.
Il problema non si manifesta con le foto con le suonerie e i video.
Ho provato di tutto a partire dal semplice riavvio del mac e del telefono, controllato e aggiornato macbook, telefono e itunes. Riparato permessi sul mac.
Cosa posso fare?
grazie
ciao

This knowledge base article may get you started: iCloud: Set up iCloud on your devices
These specific articles may be helpful as well:
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Synchronizing deletions between iBooks and iTunes: bug?

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