Starting with Configuration Manager 1511 and later, you’ll want to include the CD.Latest folder in your files backup.
https://technet.microsoft.com/en-us/library/mt605292.aspx#bkmk_Cdlatest
The site maintenance task backup will include this folder as part of its backup.
Now, if we could only use SQL Server native backup with compression for the backup task, we’d have a winning combination. Brian Mason noted that here in uservoice:
Related post here:
http://gerryhampsoncm.blogspot.com/2015/12/configuration-manager-1511-important.html
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