Microsoft has gone and made a change to how they handle some of their email filtering when using a third-party cloud service! The old method, relying upon Mail Flow Rules to bypass email filtering for mail that passed through MailRoute, and to stop people from sending mail that bypasses us is no longer the preferred methodology.

Microsoft talks about some of this stuff in their article Managing mail flow using a third-party cloud service with Exchange Online

We need to delete those two rules, add a new Inbound transport, and then configure Advanced Filtering for Connectors in Exchange Online.

This will help prevent MS from sending mail to the Office Quarantine, and improve the accuracy of filtering overall.

Attached is an overly-detailed step-by-step description of everything you need to do. It's not as bad as it looks :)

We're going to do these things in order:

Delete the old rules.
Configure an Inbound Transport in Exchange online to allow Office 365 to identify that your mail is coming from a trusted partner who is doing email filtering for you
Configure Advanced Filtering for Connectors in Exchange Online to improve your filtering and reduce false-positives on the Microsoft side

Step 1. Delete the old Mail Flow Rules

Visit https://admin.exchange.microsoft.com/#/transportrules
Delete each of the rules, by selecting a rule, and then hitting the delete button:

Step 2. Configure Inbound Transport

Microsoft uses an inbound Transport to identify email that comes in via MailRoute to prevent false-positives from their own email filtering.

Visit https://admin.exchange.microsoft.com/#/connectors to manage your connectors.
Click Add a connector
Choose Partner organization and click Next:
Give your connector a name like MailRoute Inbound, be sure Turn it on is selected, and then click Next:
In Authenticating sent email, choose the option By verifying that the sender domain matches one of the following domains, enter *.mailroute.net and click the + (plus) icon to add this sender domain. After it's added, click Next:
In Security restrictions, choose the checkboxes Reject email messages if they aren't sent over TLS and And require that the subject name on the certificate that the partner uses to authenticate with Office 365 matches this domain name and enter *.mailroute.net into the text field, and then click Next:
In Review connector, verify that everything looks good, and then click Create connector:

Step 3. Configure Advanced Filtering for Connectors in Exchange Online

This will reduce false-positives on Microsoft's side and improve filtering effectiveness. It also prevents people from bypassing MailRoute and sending email directly to you without filtering.

Microsoft has an article explaining how it all works at https://learn.microsoft.com/en-us/exchange/mail-flow-best-practices/use-connectors-to-configure-mail-flow/enhanced-filtering-for-connectors#what-happens-when-you-enable-enhanced-filtering-for-connectors

Jump right to the configuration page at https://security.microsoft.com/skiplisting
Click on your MailRoute Inbound connector
Choose Skip these IP addresses..., enter 199.89.0.0/21 into the text area, and then choose Apply to the entire organization, and click Save: