The item the doctor prescribes and the item the pharmacy dispenses are the same record. Not two lists kept in step, one list.
Two lists always diverge. The clinic adds a brand to the prescription list, the pharmacy adds it to stock under a slightly different name, and within a month the interaction check is running against a drug nobody dispenses.
This is why stock affects prescribing
If an item is out of stock the doctor can see it while prescribing, and choose rather than discover it at the counter.