I keep getting an error message when rules are applied to certain emails, the rules move mail to folders from any mail box setup to the folders which are setup on one email account

I had a similar problem almost a year ago with one of my accounts when I was trying to move messages received to a mail folder I had set up under my iCloud account. In my case, it was a temporary incompatibility between the version of mail (developer beta of macOS installed) and SmallCubed MailSuite. It was trying to move to a folder, but the folder was no longer in the original location. The folder had the same name, and it appeared in the rule correctly, but when I clicked on the Move Message to Mailbox dropdown, it switched to No Mailbox Selected. Once I added it back I stopped seeing that error.

I hope you are able to resolve your issue. If I remember any other details about what I tried I will let you know.

Give this a try: boot into Safe Mode according to How to use safe mode on your Mac and test to see if the problem persists. Reboot normally and test again.

NOTE: Safe Mode boot can take up to 3 - 5 minutes as it's doing the following; 

• Verifies your startup disk and attempts to repair directory issues, if needed

• Loads only required kernel extensions (prevents 3rd party kernel/extensions from loading)

• Prevents Startup Items and Login Items from opening automatically

• Disables user-installed fonts 

• Deletes font caches, kernel cache, and other system cache files

I think we could use a little more detail if you can possibly provide it. I can make some assumptions that you have multiple email accounts, but you have a rule or rules that if a message, regardless of the account receiving the email, matches it is moved to another IMAP account's folder? Are you using Apple's Mail or another email client?

For example, I'm using Mail.app and I have a mac.com and Gmail address. I have rules that will move emails received on my Gmail account to a subfolder under my mac.com account. Is your situation similar and is that where the error is occurring?

I'm sorry that this is a continuing issue for you. The only time I have seen something similar was when there was an issue creating the folder structure on the IMAP server. I would try and create a local mailbox folder as a test and modify one of your rules to move messages to that local folder (I know this is not what you want, especially long-term but just to see how mail behaves). If this rule holds and works consistently in a manner you expect, then we can probably rule out an issue with Apple Mail. I am assuming that you have no Mail extensions or other plugins like MailSuite.

If that does work, I'd log into the web interface of my IMAP account (so, Apple's iCloud Mail for example) and see if your folders actually exist there.

The only other thing I can think of is that there is another instance of your mail that might be overwriting your changes.

I'm sorry I can't be of more help.

I'm glad that you were able to resolve your issue.