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I have an APFS container with the following volumes:

Host:~ user$ diskutil apfs list
APFS Container (1 found)
|
+-- Container disk1 1A6DB817-9F40-47C2-9DFF-2E897D65F5C4
    ====================================================
    APFS Container Reference:     disk1
    Size (Capacity Ceiling):      703971880960 B (704.0 GB)
    Capacity In Use By Volumes:   686352678912 B (686.4 GB) (97.5% used)
    Capacity Not Allocated:       17619202048 B (17.6 GB) (2.5% free)
    |
    +-< Physical Store disk0s2 A5FA69BD-300C-4AD3-BED3-6D782ED4FD10
    |   -----------------------------------------------------------
    |   APFS Physical Store Disk:   disk0s2
    |   Size:                       703971880960 B (704.0 GB)
    |
    +-> Volume disk1s1 6B671E03-2EE3-3970-8BC9-10C4B907724B
    |   ---------------------------------------------------
    |   APFS Volume Disk (Role):   disk1s1 (No specific role)
    |   Name:                      Macintosh HD (Case-insensitive)
    |   Mount Point:               /
    |   Capacity Consumed:         685637419008 B (685.6 GB)
    |   FileVault:                 No
    |
    +-> Volume disk1s2 43856F67-ABAB-4F0F-8086-5201D65C0BED
    |   ---------------------------------------------------
    |   APFS Volume Disk (Role):   disk1s2 (Preboot)
    |   Name:                      Preboot (Case-insensitive)
    |   Mount Point:               Not Mounted
    |   Capacity Consumed:         27234304 B (27.2 MB)
    |   FileVault:                 No
    |
    +-> Volume disk1s3 B20F3C2E-8E13-4812-B52B-03077D401136
    |   ---------------------------------------------------
    |   APFS Volume Disk (Role):   disk1s3 (Recovery)
    |   Name:                      Recovery (Case-insensitive)
    |   Mount Point:               Not Mounted
    |   Capacity Consumed:         507555840 B (507.6 MB)
    |   FileVault:                 No
    |
    +-> Volume disk1s4 A57638A8-1360-4C8C-87E7-A17403DA001A
        ---------------------------------------------------
        APFS Volume Disk (Role):   disk1s4 (VM)
        Name:                      VM (Case-insensitive)
        Mount Point:               /private/var/vm
        Capacity Consumed:         24576 B (24.6 KB)
        FileVault:                 No

Macintosh HD volume takes up most of the space. It makes sense that Capacity In Use By Volumes: is 97.5%. However, if I delete the Macintosh HD volume, the container still indicates that the space is used:

Host:~ user$ diskutil apfs list
APFS Container (1 found)
|
+-- Container disk3 1A6DB817-9F40-47C2-9DFF-2E897D65F5C4
    ====================================================
    APFS Container Reference:     disk3
    Size (Capacity Ceiling):      703971880960 B (704.0 GB)
    Capacity In Use By Volumes:   684712513536 B (684.7 GB) (97.3% used)
    Capacity Not Allocated:       19259367424 B (19.3 GB) (2.7% free)
    |
    +-< Physical Store disk0s2 A5FA69BD-300C-4AD3-BED3-6D782ED4FD10
    |   -----------------------------------------------------------
    |   APFS Physical Store Disk:   disk0s2
    |   Size:                       703971880960 B (704.0 GB)
    |
    +-> Volume disk3s2 43856F67-ABAB-4F0F-8086-5201D65C0BED
    |   ---------------------------------------------------
    |   APFS Volume Disk (Role):   disk3s2 (Preboot)
    |   Name:                      Preboot (Case-insensitive)
    |   Mount Point:               Not Mounted
    |   Capacity Consumed:         20480 B (20.5 KB)
    |   FileVault:                 No
    |
    +-> Volume disk3s3 B20F3C2E-8E13-4812-B52B-03077D401136
    |   ---------------------------------------------------
    |   APFS Volume Disk (Role):   disk3s3 (Recovery)
    |   Name:                      Recovery (Case-insensitive)
    |   Mount Point:               Not Mounted
    |   Capacity Consumed:         507555840 B (507.6 MB)
    |   FileVault:                 No
    |
    +-> Volume disk3s4 A57638A8-1360-4C8C-87E7-A17403DA001A
        ---------------------------------------------------
        APFS Volume Disk (Role):   disk3s4 (VM)
        Name:                      VM (Case-insensitive)
        Mount Point:               Not Mounted
        Capacity Consumed:         24576 B (24.6 KB)
        FileVault:                 No

Why is this?

I did notice that when I ran fsck_apfs, it gave warnings that there were overallocations, but it ended by saying the volume was OK.

So now I'm running fsck_apfs -o -y /dev/disk0s2. It's been scrolling by, fixing thousands of overallocations. Interesting.

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