If you have not maintained the GL determination for Subtransaction type 01 then you are supposed to get an Error message while Posting Excise document in J1IEX after Canceling the 101 Material document in MIGO. Could you confirm this.
Please follow the below procedure for canceling the Excise invoice (For a Scenario where Part 1 and Part 2 are Posted)
First Cancel the Material document in MIGO transaction (Do not use MBST)
Post the Excise invoice in J1IEX.
Cancel the Excise invoice in J1IEX.
Can you check whether Part 2 is reversed by any chance. Also check what is the Status of the Excise invoice (J_1IEXCHDR, J_1IEXCDTL and J_1IGRXREF) tables.