I do regular backups of my HyperV host system, including the folders with the hyper v guests.
Should I also do a backup of the guests separately (e.g. from within the guest OS itself)?
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It definitely is possible to make a backup of the host in such a way as to be confident in the integrity of your virtual machines, but only if your backup software is designed for this particular scenario.
I personally use and recommend BackupAssist, which has a very convenient Hyper-V Granular Restore feature to solve the "image-within-an-image" problem.
Of course, the usual disclaimers apply: