Library synch issue

I have two user accounts on my MacBook Pro and one itunes library on an external drive, this drive is dedicated to my iTunes library
- both are pointing to the same location (/Volumes/iTunes) however they are not in sync. One says all my apps are up to date. The other says I have 200 apps needing to be updated. How do I resolve this?
I have a one year old MBP, running 10.9.5, the external drive is a 1 TB with 300 GB space left on it.

And before anyone asks - no, the disk was not erased as part of the screwed up upgrade.

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