Yes! I suggest you do not place a copy of your scenery build, into the Community folder, because unless you have scenery duplicates, that is clearly what is happening. Please consider the Virtual File System, does everything you need, to see, or edit scenery in real time. Therefore, the only reason to place a scenery build into the Community folder, is to see it, while not in DevMode. This means, when you do build the scenery into the VFS, there are now two of everything, the "solid" non editable version in the Community folder and the one in the VFS, from which you can delete stands.
The good news is that you can just ignore all this crap, if you make the changes, save and build, quit the sim, delete the previous version of the scenery from the Community folder and then add your new version from the Project Packages folder, the changes will have been made. However, it is less confusing, to simply delete the Community folder copy of the scenery, before beginning an edit, imo.