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I have installed MS Project server 2013 and Integrated it with MS SharePoint 2013

and I created a Project Web App with SharePoint permission mode.

Now I want to Change from SharePoint Permission Mode to Project Server Permission Mode

In Microsoft Site it said that if you change from SharePoint Permission Mode to Project Server Permission Mode it will delete all security groups.

I did not understand it would it delete all security groups related to this Project web App I created or it will delete other sites collections security group also.

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In our case no SharePoint group (neither standard Project Server, nor custom one) was deleted, when we transformed the permission mode to the Project Server mode via:

Set-SPProjectPermissionMode –Url http://YourProjectServer/PWA -AdministratorAccount domain\adminuser -Mode ProjectServer

It is suggested however, to create a backup from the SharePoint content DB as well as from the Project Server service DB before performing the permission mode migration.

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All the security group in your ProjectWebApp (URL which you provide while running command Set-SPProjectPermissionMode) will be lost. Basically, no user apart from Project Service account will have access to the site when you change the permission mode. You will have to re-assign all permissions. This will happen whenever you switch the permission mode.

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