Money in banks is in the end just information stored in ledges about who owns who money. If a transaction occur within a bank it just numbers of one account getting an relative change to an other account. If an transaction occur between banks, the banks has a relation and the bank own ledger get changed, in addition to the individual accounts. With a clearing house you add a middle man that takes up part of the risk if either bank would fail in their obligation to honor the ledger. The actually movement of physical funds and valuables is quite rare and don't general occur from single transactions.
If you can't transfer the information then the system of transferring information stored in ledges stop working. One can go out-of-band, but that assumes the other party is also willing to do so, and that there is no law/agreement against by-passing sanctions.