Allowing pharmacists to accept prescriptions from patients, enter them in the computer, and file them according to the date they were entered has advantages.  Many prescriptions are misplaced by patients when they don't have them filled and this creates a great deal of confusion when a fill is needed.  The pharmacy contacts the prescriber for a refill, the prescriber states that they gave one to the patient, the pharmacy attempts to contact the patient back asking for a prescription the prescriber gave them months ago.  And the search begins.

In many cases, the new "on hold" prescription can be linked to the previous RX allowing a seamless fill for the pharmacy and the patient. 

An on hold prescription should go through the same checks that a filled prescription does, a pharmacist needs to review the information and sign off that it is indeed correct regardless of who does that data entry. When the prescription is needed, it will be treated as if it was a refill.

Pharmacies that are accepting these prescriptions from their patients for convenience have to do twice the work, because they have to retrieve that original prescription, deactivate it, update the number again, fill it and re-file just so it is filed in the right place!  The same thing would occur if a patient doesn't pick up a prescription in a timely manner and it is returned to stock, only to want it filled again at a later date.  It is redundant and over burdensome on pharmacy staff.

The regulation stating that prescriptions must be filed in chronological order from the date filled is simply left over from a time before computers.  That made the most logical sense at that point in time.  With today's data bases we can pull information out in a variety of ways.   We can search by patient, prescriber, medication, date filled, date written, etc.  Retrieving information is no longer limited. 

There is no good reason to file prescriptions by date filled any longer.