Hi and welcome to JustAnswer:
Having a self directed IRA provides investment flexibility. However, along with the increased flexibility you are bound by the policies of the trustee.
How can the note still be at $32K if $16K has be repaid?
Your best option is to find another attorney that may be more reasonable in fees. The attorney should understand the specific situation to assist in determining fees and collectability of note.
While the remaining partner paid only 50% of the note, your loan was to the partnership and you can attempt to collect the full amount of note from either partner or both. It is then up to the payor to attempt collection from the absconding partner rather than you.