I recall last year sometime I used the Wipe Free Space feature on an old laptop with an HDD drive. While this feature did increase my overall storage capacity, I found it resulted in the HDD running considerably slower even after I tried various options like Optimize, Defrag and more. I even reinstalled Windows from my factory partition.
I don't know if what I experienced is in any way related to the current issue, although I see in the notes mentioning the reason for temporarily disabling is that this feature is deleting more than it should.