After hours upon hours of testing every combination, it seems that once the 16x is split between slot 5 and 6 (to x8x8) it cannot be split again to x4x4.
I also wanted to confirm that auto splitting works fine when using an x8 and x16 card however not when using an AOC-SLG3-2M2 in slot5 while slot6 is populated. This card works great in slot 3.
https://www.supermicro.com/en/products/accessories/addon/AOC-SLG3-2M2.php