@werdi As far as I know the folder issue was resolved about a week ago . Please see the link here
And the release of 2 days ago, will have this included. It was tested by myself and pamtbaau.
https://getgrav.org/ or update through the admin panel.
How did you get on with your clean test server ?
The only thing you will have to check is any numeric pages / folders are in a low numeric order, as if there is one of these high numbers 1000000 or 9999999, when adding additional page it will use these numbers + 1
Come back to us, if you need any more info