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I have a Sharepoint site with a number of web applications (that are relatively large). I need to decommission the Sharepoint site and database servers and install SharePoint from scratch to a new different server.

Should I perform a full farm backup and restore the backup at once? Or should I perform Web application backups and restore the web applications one by one.

What is the recommeded approach / pros and cons please?

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A complete migration depends on the components you have in your SharePoint farm.

By components I refer to the following that should account in your migration strategy.

WSP
Web Config Entries
Layouts
folder Site Backups
Service Application Backups
Farm Backups
Content Database Backups
Other customizations

To keep it short here are the scenarios that will help you decide the type of migration you want

For performance and stability concerns , personally I would always go for the second option. SQL Backups of database and attach driven restore performs 100 times faster than site backup restore.

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