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We have an issue where periodically (monthly it seems) some users will lose specifically granted 'contribute' permissions to certain subsites in our SharePoint environment. I did some research and found one blog that suggested the culprit could be 'duplicate' user entries in the UserInfo table of the content database. The profile import/timer job, the blog claims, does some sort of housekeeping which then removes all of the user's permissions, due to the 'deleted' record.

I looked in our UserInfo table and I see that the two users I have problems with do have duplicate records for the same site, however one record is marked as deleted and not active and the other is marked as active and not deleted. From what I have read elsewhere, that should be just fine, so I hesitate to write an app to delete the 'deleted' record. I was hoping to find a more definitive answer to this question before we go mucking around with the data.

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I had a similar issue where we had users that existed on two different domains. It depended on how a user logged into SharePoint - and what account was given the access. It was messy until we forced the domain prefix on login!

This might not be the source of your issue, so maybe this question and answer will help you:

SharePoint 2013 Duplicate User Profiles

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