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I want to update macOS to High Sierra. This question is for precaution purpose before updating macOS.

I have two drives : SSD-Primary and HDD-Secondary

macOS is installed in SSD and HDD is for backup purpose.

Will High Sierra also convert secondary drive into APFS automatically, when I upgrade macOS to High Sierra installed on primary drive?

Should I disconnect secondary drive before the upgrade?

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From the APFS Guide FAQ:

How do I upgrade to Apple File System?

The macOS High Sierra installer offers nondestructive in-place upgrades from HFS+ to APFS for bootable volumes. You can use Disk Utility to convert external volumes from HFS+ to APFS format.

(Emphasis mine)

Your secondary HDD is not a bootable volume (assuming it not a clone) so it will not convert unless you do so manually.

That doesn't mean your HDD can't use APFS.

Can I boot macOS High Sierra from an APFS-formatted hard disk?

Yes. macOS High Sierra supports Apple File System for both bootable and data volumes.

You will have to convert the second HDD after-the-fact.

But since you this question is getting info, (like you said) as a precaution, the best advice is to make a full backup before proceeding.

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I would check that both drives are backed up and then install the OS with your normal setup intact and all drives connected. This lets the scripts see all your apps and in case you store photos or other system / user files on the other drives, any migration steps can run on that data.

All Apple installs are now archive and upgrade where the installer runs pre-install checks, pre-install scripts, makes a new system and then runs migration and post install cleanup scripts to move all your settings to the new system.

The APFS conversion is only for SSD exclusive boot system drives and nothing else converts automatically for 10.13.0 release. Fusion drives and HDD stay on HFS+ for the initial fall 2017 builds of High Sierra.

If you’re not sure you’re ready for this full install, consider installing onto an external drive and testing.

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