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We wanted to back up site collections from PRODUCTION to DEV via PowerShell Backup-SPSite and Restore-SPSite and encountered this problem:
restore-spsite failed by DirectoryNotFoundException
ULS Logs suggested the following:

Could not deserialize site from E:\***\***\***.bak . Microsoft.SharePoint.SPException: Schema version of backup 15.0.4569.1000 does not match current schema version 15.0.4420.1017     at Microsoft.SharePoint.SPSite.Restore(String filename, Boolean isADMode, Boolean& readOnlyMode, Boolean& hadWriteLock)
Resolution:
So from the above we at least had the idea that SharePoint is reporting some kind of version mismatch. But from CA is was apparent that this is not configuration mismatch. So it has to be a content database issue. We first determined what database the target site collection is going to be at. This can only be done by creating the target site collection before hands. And then we tried a restore. The restore failed. Now we upgraded the entire database by:

Upgrade-SPContentDatabase DatabaseName
It took a while but it upgraded the database.
After this we tried the restore again with force parameter enabled. And it worked this time.

For details, please look into my forum post:
https://social.technet.microsoft.com/Forums/en-US/a57b742c-ca20-4471-bdab-6edc1fea18f1/restorespsite-failed-by-directorynotfoundexception?forum=sharepointadmin

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