I think he is referring to the S3D index:
As usual though, I could well be wrong... lol - Some of what Hebe found is from the hex-editing days. Silent3Ditor will not let you save a dat file without first updating the index, which it does automatically when you save, or you can initiate it yourself. S3D also does ID checks and will let you know if there are conflicts there. None of that functionality is available with hex-editing. That is up to the user. The empty 3D objects are also part of the hex-editing, as are a few other little "tricks" that hex-editing people employed to "mark" their files.
As for "automatically" removing such items, it is possible, but would involve some deep programming skills, which are hard to find these days in the "hobby" world. Hebe might be able to pull it off, but he has other, more important chores to do with his mySH3-Tool first...
- which is something every modder should have in their toolbox, and use on a regular basis...
