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Hi David,
We understand that the filter will be rested after opening a file in document libraries with many files.
We tested at our end, but we are sorry that we are unbale to reproduce this behavior at our end even we refresh the library page. And I believe that is because we don’t have the same environment as you. To work normally and efficiently for now, please create the specific View to filter all the documents.
Since this issue happens to multiple users in a complex environment, I sincerely suggest you contact IT admin to raise a ticket in Office 365 admin center->New Service Request. The related team will involve more resources and help you check it.
For your reference: Ways to contact support for business products - Admin Help
You can contact us if you have any other concerns.
Best Regards,
Ivy