When I run Disk Utility against my Data drive on my MacBook Pro, I get about a million of these errors:
error: doc-id tree: record exists for doc-id 18164/0, Tile-ld 485842098 but
no inode references this doc-id
error: doc-id tree: record exists for doc-id 1816483, file-id 486368757 but
no inode references this doc-id
error: doc-id tree: record exists for doc-id 1816484, file-id 486385532 but
no inode references this doc-id
error: doc-id tree: record exists for doc-id 1816489, file-id 486476281 but
no inode references this doc-id
error: doc-id tree: record exists for doc-id 1817820, file-id 501182195 but
no inode references this doc-id
Checking the extent ref tree.
Neither Disk Utility nor fsck can repair the issues in normal or Safe Boot. Any other suggestions before I run Super Duper! and do a full backup, reformat the drive, reinstall the OS, and restore from the backup?
Have you tried running Disk Utility/Disk First Aid from macOS Recovery instead of from a normal or Safe Boot? And run it first on the container that has the bootable system and Data volume, then on individual volumes within the container?
First, make sure you have a full backup in case you need it for recovery.
Please show the relevant sections (internal physical disk and its synthesized container) from the Terminal command diskutil list.
With the system disk there are 4 levels for doing repair: Physical disk, Container, Volume Group, and Volume. Try all four, in that order, from Recovery.
