remember, Avid will always output to a “1” folder until it is too full. Then it will switch to “2” unless you have a 2 that is too full, and so on.
The fact that your highest numbered folder might be 564 is not important to Avid. If there is no “1” folder it will make it, and render to it. If there is a “1” folder with room, it will render to it, and so on and so on. It doesn’t know you want to use 564, and you can’t tell it that.
If you were getting duplicated media files, perhaps you were consolidating, without the “skip media already on the drive” checkbox clicked? I believe the MOB files you are pointing to are usually internally created avid files, like renders created in the process.
Glenn