1

I got a datastore which consists of 2 partitions on different hdds. I freed enough space to store everything in the datastore on the first hdd.

How can I move all data to the first partition and remove the second one from the datastore?

2

An extent can never be removed from a datastore. See here.

To get the single partition into a datastore by itself, you'll need to move all VMs off the datastore temporarily, destroy and re-create it as a new datastore, then move the VMs back.

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