I have a problem on windows when I connect via webdav, in practice, not all the files are displayed but only a part, this does not happen on mac os.
Native webdav in windows is not working that well. On the documentation there is a pull request that is supposed to work better: https://github.com/nextcloud/documentation/pull/1505
I can’t remember to have heard that just a few files are not displayed. In this case you have to be more specific, if these names have something in common, certain extensions etc. There have been issues with files starting with a space.