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We have what we initially thought was a bug, but after some ILSpy'ing I determined it was intended behaviour:

Basically, user access is currently a manual process for project sites/workspaces on top of the resources added to the project site automatically based on their categorization/task assignments, etc.

However, whenever a workspace sync kicks off it will first REMOVE the SharePoint user from the site and then subsequently re-add them with the project server permission level that applies to them. This becomes an issue when this user has already been manually added to the project workspace site with an even greater permission level.

We're currently on SP1 - has this been corrected in a later CU? Should we look at workspace permission management as an all or nothing approach? (either all manual, disable all workspace syncs or little to no manual and let PWA handle all access)

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Did you find any solution to this? We're experiencing this same problem with a customer, but from a performance perspective. They have a relatively large number of sites (500) and a large resource pool (500-1000), and they are hitting performance issues because of how inefficiently the permissions are removed for each person, before being each added again, regardless of whether their permissions have actually changed since the last sync... so is there a CU that does this better? –  Ashley Steel Jul 24 '13 at 8:56

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Seeing Ashley's comment prompted me to answer my own question:

I ended up disabling automatic user synchronization against Project Sites using the UserSyncSetting enumeration: http://technet.microsoft.com/en-us/library/hh670402(v=office.14).aspx

In my case, I set this to '2'. This allows project site access management to be governed and controlled by the stakeholders instead of automatically by Project Server.

If you still require some automated synchronization of users to project sites but without a huge performance hit, the best compromise seems to be to make sure project sites are subsites of your PWA site and then disable the project site synchronization using the technique above. This way the users & permissions applied by the PWA synchronization are inherited down to your project sites. In Ashley's case, this would mean one site being synchronized over 500.

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