SK53
(SK53)
3
I also think you are confusing OSM editors with general GIS software. Try QGIS.
The OSM data model DOES NOT HAVE LAYERS: therefore a layer oriented editor is not going to work.
Hydrology, landuse, highways, buildings etc are all inter-related within OSM. As @GerdP says you can use JOSM and edit in layers (and you can use purge to remove features within the edited layer), but you will always have to edit things in relation to everything else. For instance if you choose waterway features and purge other features in an area, you may inadvertently edit things like political boundaries which share data with waterways. This may be fine, but it might not be fine as although the water course might have changed, the boundaries might not. In addition handling conflicts between different versions of the same object is non-trivial.