The installer removes outdated scenery and we have new installers for the scenery to restore it. It is correct that we remove all IPACS scenery which is required for the update to work correctly. So this is intentional and necessary.
The issue is that third party and user made scenery were installed in the same directory which our installer is unaware of. We always emphasize to never ever install anything custom into the default installation folders because it may be affected by automated processes such as installing a new update or by just running Aerofly FS. But we lack authority or control to ensure that this doesn't happen because in the end it's an open platform that accepts new paths in the root folder.
If you own a third party product and it doesn't allow you to change the path and it installes into the root directory and not into the Add On directory then please contact their support as well. Or let us know which products these were exactly so we can contact them.