iTunes Media folder

I have my iTunes library on an external drive with the default folder named as iTunes Media. I suddenly find that the majority of my library is now in the iTunes main folder while the remainder is in the iTunes Media folder. I am pretty certain that the Media folder is the default. Why is my library split without my changing the default folder? Does it make a difference where the files are stored? I am currently transferring all the files to the iTunes Media folder and will reset the default location when the transfers are finished. Does anyone know why this has happened? Any help would be greatly appreciated as I have approximately 230,000 files ( nearly 2 terabytes) in my library and would hate to lose any of them. I do a backup every night to another external drive.