Issues with PO cancellation

HI,

I have some queries on PO cancellation:

1) We are seeing some cancelled orders that are still showing at Open Commitments in the JC module?  They have the status of 999 but the amounts are not being taken out of the project? 

2) How can we close purchase orders which have been partially delivered as this may have caused the issue in the first place? OAR attached.

Also attached are the screen prints from Commitment Inquiry.