DiskUtility inode warnings wont clear up with FirstAde

Hello everyone,

I am running 14.0 (23A344) and have sporadic issues like operation not being permitted when trying to remove some folders in ~/Library after some application was uninstalled using AppCleaner.app, which I have used for years. It works 99% of the time, but sometimes I get errors that some files/folders in ~/Library can not be removed. If I try to "sudo rm -rf" that folder from Terminal, I get operation not permitted.

So this did bring me to DiskUtility. I am running MBP 14 M1 Pro. As always when I get a new machine, the first thing I do is reformat SSD to Case Sensitive Encrypted from default Case Insensitive since that gives me issues with my source code compilation when developed between Mac and Linux.

Here is my Disk Util. I do not get any warnings on any other partitions/sections under and including "Macintosh HD volume" at the top of the hierarchy.

When I run FirstAid on the Data partition, I get the following warnings.

Now I can run this repeatedly, and the same errors are produced. I can do a reboot in between running Disk Utilities, and the same warnings. I did boot to Safe Mode and run Disk Utility, and the same warnings.

I contacted Apple support and have a case: 102125788648, but I was also instructed to create a case here.

Here is my side story, why I can not use Time Machine.

As a last resort, I was asked to reformat and reinstall. That is not an option for me at this point since restoring everything is a 1-2 day job.

Now, I know there is a Time Machine, but on my two attempts in the past, backups created on brand new external Samsung 970 Pro SSD failed to restore. These two backups/restores were a few months apart. So on the second support call, it was suggested by support to back/restore using TimeMachine. After stating that I had a horror story on my first attempt a few months back, I was assured that the issue had been fixed and I should not have an issue. Oh well, same issue. After spending considerable time with support (a few folks) they noticed that the Time Machine folder structure was wrong and some intermediate folder was missing causing the issue. In both cases, I never heard anything back if it was addressed/fixed, except the support during the second case, assured me that it was fixed. That is why I did try to use Time Machine with him to back up while he was screensharing to make sure I did not do anything unusual. Still, restoration failed.

So even Time Machine should make restoration painless, for it was pain, since on the first occasion I lost all the files. On second I could brow Time Machine folders in Terminal and pick files/folders from there. Took a long time. And to throw another strange case, I could only access them from Terminal under my wife's machine which is running an older Mac, but the new restored Mac I "was not able"! which is very weird. Both machines were at the time Intel machines. So I never attempted to use TimeMachine again on M1 Pro.

So I hope everyone sees why I do not want to reformat and restore.

Now, I have a feeling that most of my problems might be related to Case Sensitive reformated SSD. I can not go back to Case Insensitive (default), as I explained above.

I am here to provide any information to help get this fixed. Any suggestions or anything to try?

Robert