This is not a bug in autower, but rather a nice hint to you that your scenery settings are wrong.
Every directory that is referenced from your scenery.cfg must contain a subfolder named scenery, where the .bgl files are stored. (There may also be a textures folder, but that's not relevant here.) Only BGL files in the scenery subfolder are actually "seen" (and thus used) by Flight Simulator. Look at the following directory layout:
+ Addon Scenery\ | +-+ scenery\ | | | +-- A.bgl | +-+ B\ | +-- B.bglIn this case, only the file A.bgl is considered by FS, B.bgl is ignored.
If you want B.bgl to be considered, you must revert to either of the following layouts:
|solution 1: merge files into a single folder||solution 2: correct directory layout|
+ Addon Scenery\ | +-+ scenery\ | +-- A.bgl | +-- B.bgl
+ Addon Scenery\ | +-+ scenery\ | | | +-- A.bgl | +-+ B\ | +-+ scenery\ | +-- B.bgl
In the latter case (solution 2), you will also need to add the directory Addon Scenery\B to your scenery.cfg, because it is not recursively considered from its parent folder.
To summarize: If there is no scenery.dat in a folder, then the contents of that folder are not considered. The scenery.dat is only created by FS if scenery BGL files are found in the scenery subfolder.