I think you are unlikely to be able to delete the tower through editing the scenery BGL's. However - by adding an alpha channel for the tower texture you should be able to "rub out" the building. You wouldn't remove the tower - you just wouldn't be able to see it.

Lol! I would have awnsered that but I havent done any transparency stuff for a while There will probably be some aircraft repainters & a Hagar around here who would be better placed to explain! This is a sort of guess!

Anyhoo - first things first I suppose is to get yourself setup with DXTbmp, download the MW GFX DLLs & DXTBmp from here (DLLs are required for DXTbmp to run) -
http://www.mnwright.btinternet.co.uk/

You may be able to add an alphamap manually in DXTbmp but if you open the texture in DXTBmp and then export this to your image editor you can add over the areas you want erased, blocks of pure green. If you then import this back into DXTbmp and find the bit related to adding an alpha channel it should convert all areas of pure green into 100% transparent.

Save the result as a DXT1 bmp in the same directory and with the same filename as the origional texture

I'm going to need some help here - I'm lost