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When restoring site template from source to target environment the custom permission doesn't copy. According to Microsoft article, this is how it behaves.

Is there any other OOB way(no code or script) to copy a site from one environment to another with custom permission?

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Unfortunately , the site template does not hold the custom permission , in this case , you will need to recreate it manually.

So if you need to move a site from source environment to destination environment with the custom permission , you should backup and restore the entire Site Collection rather than using the site template as the following :

  • Take a backup of site collection from the old web application.
Backup-SPSite -Identity http://siteURL -Path "C:\\MoveSiteCollection.bak"
  • Create a new web application .

  • Restore backup in the new web application.

Restore-SPSite -Identity http://url -Path "C:\MoveSiteCollection.bak"

For more details check

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  • I want to copy site from source environment to target site collection as a sub site. I cant copy site collection and restore at target environment. – Madi Oct 25 '16 at 4:17
  • Dear @Madi unfortunately , site template did not hold custom permission ,You'll need to manually recreate it . the custom permission can backup if you take a backup for the entire site collection as I mentioned above – Mohamed El-Qassas MVP Oct 25 '16 at 8:09
  • Thanks @M.Qassas, The command you mention back up and restore site collection. Is there any command to back up and restore site with custom permission? – Madi Oct 26 '16 at 0:34
  • try to export and import as this Export-SPWeb -identity "URL/sites/subsiteToBeExported" -Path "LocationToStoreExport\exportname.cmp" -includeUserSecurity note : IncludeUserSecurity Preserves the user security settings except for SPLists that have broken inheritance and item level permissions set. – Mohamed El-Qassas MVP Oct 26 '16 at 7:12
  • also check the details parameter for import and export command at technet.microsoft.com/en-us/library/ff607895.aspx , please don't hesitate to tell me if you need any clarification – Mohamed El-Qassas MVP Oct 26 '16 at 7:18

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