Mac Mail - Flagged emails create a 2nd colour flag. How to stop it?

Honestly, never every have I seen such an issue in Catalina, Big Sur or Monterey.

Can I suggest some Trouble Shoot Steps but whether this will actually solve this issue we can one experiment.

None of the steps will doe any Harm to the Computer or the Big Sur 11.7 (Recent update and good that is done 👍)

1 - Restart in Safe Mode. This will perform a Disk Repair, clear cache files and only load Apple Software, extensions and fonts. The boot up will be slow and can take some time - Normal.

2 - Does the issue present in this mode ?

3 - Sometimes a Safe Boot followed by a Normal Boot will just put things right.

4 - If not - there could be something in the main User Account playing up. To further isolate this - Set up users, guests, and groups on Mac. Then log out of the Main User account and log into the dummy account and test again if the issue persists.

5 - If the issue is present in the dummy account - then, this appears to be a System Wide issue on the computer.

6 - Understand, we are all working Remotely from all around the world. 

Therefore, we do not have the On-Hands experience the User ( you ) has with this computer.

The next best thing for us to having a semi - actual On-Hand experience on this computer is to follow the steps below

Download the Application Etrecheck directly from the Developer.

The application is free or paid from added features. 

It will take a Snap Shot -  both the hardware and software.

 The Report will Not Reveal Any Personal Information. 

Post back the Full Report - copy and paste - using the Additional Text Icon ( 3rd Icon to last )

We can have a look at the report for possible issues and may have possible suggestions to resolve the issues.

Description: Issue with Mac Mail showing two colours of flags (on flagged emails) even though only one colour of flag is selected. 

https://apple.stackexchange.com/questions/379736/mail-showing-incorrect-number-of-flagged-emails

• Quit Mail if it’s open.

• In ~/Library/Mail/V8/MailData, delete any file that begins with “Envelope Index,” such as Envelope Index or Envelope Index-shm.

• Your home Library folder is hidden by default. To display it, choose Finder > “Go to Folder” and then enter “~/Library”

• Open Mail.

• Mail creates new Envelope Index files. This process may take a few minutes, depending on how many messages Mail is reindexing.

Major Issues:

Q -  No Time Machine backup - Time Machine backup not found.

A - One may have some other means to Safe Guard the Important Personal Files. Though, as per presented information, any and all important Personal Data is unprotected and at risk of permanent loss.

Q - System Integrity Protection disabled - System Integrity Protection is disabled. This computer is at risk of malware infection.

Q - System Integrity Protection: unknown (Custom Configuration)

Q - Kernel boot arguments - This computer has custom kernel boot arguments.

Q -  Boot args: keepsyms=1 debug=0x100

A - If Apple wanted the computer to run without SIP Enabled on an ongoing basis, they would not have introduced this Security Feature into Big Sur. It is ok to have SIP Off but only for the time needed to perform some special Actions. There after,  to Enable the protection feature —> SIP 

Q - Apple security disabled - Apple security software is disabled. This computer is at risk of malware infection.

A - User choice

Minor Issues:

Q - High battery cycle count - Your battery may be losing capacity.

Q - Battery: Health = Normal - Cycle count = 1016

A - Batteries are considered Consumable Products. Over time it will degrade to a point where it needs to be replaced. The usage is normal as the capacity will go up and down all the time and never stay always at 100%. Apple Batteries are rated for 1000 Full Battery Cycles and / or 80% Capacity before needing Evaluation or replacement.

Q - Unsigned files - There are unsigned software files installed. These files could be old, incompatible, and cause problems. They should be reviewed.

A - Self explanatory and worthy of consideration to update / upgrade or outright replace certain applications with those more Big Sur compatible 

Welcome.

Have been testing my own Flag System on macOS Monterey 12.6 in attempt to further dissect your Flag System Issue.

Below are 5 Orange Flagged e-mail in Archive Folder and with the Flag Category expended

Here I have Flagged 1 e-mail in Inbox as Purple and still have the 5 Orange in Archives and Flag Category expanded

Here I Removed the Purple Flag on the Specific e-mail itself and keep the Flags for Orange E-mail and Flag Category expended

The Purple Category remains though .. . Drum roll please (lol)

Collapse the Flag Category . . . . next

Re-Open the Flag Category -- > the Purple Category has vanished 😀

T.Edwards wrote:

Hi P.Philip, thanks for persevering on this.

So a couple of things :

1) When you flag emails the same colour (for example orange) it shouldn't create a drop-down arrow with a sub-section called Orange. It should just change the wording from Flagged > Orange (as there is no need for a flag section when they are all the same colour)

A - Correct

) I also tested how you did, and have a 2nd flag coloured Purple, and if I did unflag that Purple email it would disappear when you un-collapse the section, but when I re-clicked into an Orange flagged email, the Purple flag (in my case it's Red) would pop right back into play (the issue I've been having)

3) I think I've found a workaround. This is to have all emailed flagged Orange, add "Orange" as a Favourites, and then rename Orange as Flagged.

4) The workaround is great, but the issue is still lurking in the background, so would be great if I could fix it.

Please see the video here of what's happening, and how the workaround works.

Any other ideas would be great.

Good video but sorry I do not see an issue

Thank you for the Report.

I will dissect it, in detail.

Will get back to you shortly

If one follows the previous Steps in the order in which they are presented I am certain the answer will be self event