I'm not sure if this was a one-off issue or if it's a reoccurring problem, but I made some custom groupings of bushes in my scenery so that I could quickly cover placement over a large area.
Once the grouping was created, I nested it within a parent group, before duplicating the child group and altering the placement. I kept doing this until I had covered the entire area around the airstrip.
I went back and tweaked placement of a few groups by selecting them individually, and was able to move them just as I had originally had them grouped. I saved the project and quit for the day.
Today I finished off adding in some 3D trees, and when I compiled the package, I was getting horrible FPS. I decided to go back and remove some of the vegetating thinking that I may have just placed too many individual models for the sim to handle, and to my surprise, I found that thousands of bushes were duplicated.
Now the logical choice here would be to just delete the groups that got duplicated, but alongside this the groups have all been mixed together. So now, while selecting a group may remove a fair bit of duplicates, it also removes non-duplicated objects..
I'm not sure if this is just a case of bad luck and something got botched on project load, or if it's something that reoccurring. Maybe it only happens with a large number of grouped objects..?
I have tested several areas of the 3D trees, which are also quite numerous, and they do not seem to have the same issue.
Edit: I found the "Remove duplicated objects" selection under Edit in the Scenery Editor. This appears to have gotten rid of the duplicates.