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This issue is directly related to the new article posted here: https://support.office.com/en-us/article/the-rules-on-this-computer-do-not-match-the-rules-on-microsoft-exchange-d032e037-b224-429e-b325-633afde9b5f0?ui=en-US&rs=en-US&ad=US: The rules on this computer do not match the rules on Microsoft Exchange.
I also have several rules disabled to run manually. When I make rule changes, I get the error messages described in that article. Also, for me, if I disable the rules in outlook.office.com it will disable them in Outlook. But once Outlook syncs back up, the rules are erased online.
I found this work around if changes need to be made to rules. Make sure you have a backup of your rules first!:
1. Open Outlook with this switch: outlook.exe /cleanserverrules. This removes all rules online.
2. If prompted to choose which set of rules to use then select CLIENT.
3. Make any changes and then click OK.
This will push your rules, including changes, up to the server. The disabled rules will be deleted online but the results are the same as those are manual rules anyway.
This works for me as I am primarily a Desktop user. If you use outlook.office.com as your primary email, and you want disabled rules, you will have to avoid using Outlook on the desktop. This is a very buggy workaround and things could go wrong. You should make a backup of your rules after any change (.rwz file).
Using the client as the primary rule source is not optimal. Making the Server rules the default would automatically back up any rules. It would protect from Outlook getting corrupted or a hard drive failure, or if you need to migrate accounts to a new tenant; the server rules would be persistent. With the online rules being broken we can't get any of those benefits.
The crux of the problem is that disabling rules, whether online or in Outlook, ultimately deletes
them in outlook.office.com and creates the mismatch.
Microsoft this needs to be fixed!