Hide spesific folder from OneDrive synk all users

We have a cloud application that uses the user's OneDrive while they are working with documents. These files are stored in a specific folder and are removed when the user checks in the files through the application. However, it seems the application does not handle users checking in files while they are syncing.
I’ve looked into policies and settings in SharePoint Online and Intune, but I haven’t found a way to exclude the folder for all users. The only solution so far seems to be guiding users to do this manually.
Is there really no other way to achieve this?