It has been a very long time since I had to do BSA CTRS. I have a daughter in law that made a deposit into her mother and father in laws joint checking account. The father in law is deceased but has not been removed from the account. do I leave Part 1 for him in the CTR or remove his information since he is deceased. The mother in law is still living.

The deceased do not benefit from cash deposits. Regardless of the delay in updating the ownership in the bank's system, this account became and individual account owned solely by mom the moment that dad passed away.

You didn't ask, but I do suggest that your bank should not allow the account to continue to appear as a joint account. Leaving the decedent's name in the account styling can lead to confusion that might result in a teller's acceptance of a jointly payable check (names conjoined by "and" or "&") or a check payable to the deceased for deposit to the account.

After a reasonable period (I suggest 30 days or less) after a joint owner's death, the bank should contact the surviving owner(s) to arrange for updating the account, to include dropping the deceased's name and, if applicable, updating the SSN used for interest reporting. If there are any recurring direct deposits to or direct debits from the account, check to see if any of them should be terminated/returned.

I am surprised that a financial institution would take such a large cash deposit without one of the signers present.

I know of a very large bank that will not allow non-signers to make deposits.