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I backed up one site collection from one WA and than I restored that in another WA as a new cite collection.
I found out that new site collection has same site ID as original site collection. This causes me major problem as I can't activate app permission for workflows.

Any help how to get new site ID in any step from backup to restore?

EDIT: I found here, that new site every time gets new ID, but this is incorrect at my case. Every time, what ever I tried I got same ID as original site.

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The Sitecollection should be getting a new ID. The webs inside it will retain the old ID's, and there is not much you can do about it if you use backup and restore to recover the Sitecollection.

You have the option to retain the Sitecollection ID by using a parameter in your restore script (PreserveSiteID)

https://docs.microsoft.com/en-us/powershell/module/sharepoint-server/restore-spsite?view=sharepoint-ps

You might try to use the export and import feature, which has some other issues (Maximum Size, not retaining all items) to move a site (not Sitecollection) to a new location.

https://docs.microsoft.com/en-us/powershell/module/sharepoint-server/export-spweb?view=sharepoint-ps

https://docs.microsoft.com/en-us/powershell/module/sharepoint-server/import-spweb?view=sharepoint-ps

edit: If you move by DB-Backup the IDs cant be changed at all

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