Don't want to synchronize with duplicate iTunes

My wife rarely uses iTunes, so I use a third party synchronizing utility (Chronosync), to make her iTunes (and her iPhoto) to be working backups of mine.    We hadn't noticed until my iMac was in the shop and I opened her iTunes, but my iPhone & iPad want to sync wirelessly with her iTunes as well as mine.
Is there a way to have her duplicate default to not synchronizing?
(We have to have only me modify iPhoto or iTunes - too bad those products aren't designed so that we could both update their data).

First check that all your settings are correct, that notes syncing (mail and notes on a computer) is checked on all devices (system preferences > iCloud on a mac and settings > iCloud on a iPhone, iPad or iPod).
Make sure the notes you are adding are added to your 'iCloud' account and not an 'On My Mac', 'On My Phone'  or other non iCloud account (you can do this by checking in accounts on an iOS device, or the left side panel in mail on a computer), non iCloud notes will not sync.
If you are sure that everything is set up correctly and your notes are in the iCloud group, you might try unchecking notes syncing (mail and notes on a computer) in the iCloud settings, restarting your device and then re-enabling notes syncing.

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