This has me pushed to my limits.
I have a few accounts that are normally turned off (disabled), which I only turn on if my client is having a problem. ANY time you make a change in Mail Preferences, if forces an alphabetization of your accounts in the inbox.
I'm so tired of submitting official bug reports on this, that I finally renamed my accounts with a (1.) (2.) etc. before them... It STILL doesn't work, because mail forces the iCloud to the top of the list... then followed by IMAP accounts... then POP accounts.
This is INCREDIBLY invasive. Trust me... I know my own workflow better than an engineer in Cupertino. I just don't understand who thought this idiocy was a good idea!
If I've taken the time to reorganize it... LEAVE IT ALONE!