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I have done migration of content db from 2010 to 2013. Now I want to upgrade site collection using Upgrade-SPSite command but problem is this site collection contain more than 100 sub sites.

Last time I did this upgrade it took more than 3 days to complete. So I was thinking if it is possible to do upgrade of only specific sites rather than whole site collection?

This way I can do let's say 10 sites at a time on weekends rather than facing 3 days downtime like before.

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    You would need to take a backup of the subsites and put them in new site collections to split them up, and then import them back to the upgraded main site collection, but this will fail if you are using workflows and stuff like that as they are stored on a site collection level (not exported with subsite). – Christoffer Sep 9 '16 at 11:28
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This is by design, upgrade run against Site collection level. You cant run it at subsite level.

I think, now time to re think the architecture of your site collection and may be split into multiple site collections. Otherwise you have to wait for 3 days and in future time will increase as content will increased.

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