In this Google Street View you can see what appear to be rails leading down into the flame trench under launch pad 39A.
What was/is the purpose of those rails?
Those are remnants of the Apollo program era when the Launch Complex 39 was built. They were used to transport large removable blast deflectors to the pad when the Saturn V and Saturn 1B launch vehicles were already transported there on the crawler-transporters.
Blast deflectors at the Complex 34 launch pad. Prior to a launch, one of the deflectors was moved into place underneath the launch pedestal. The rails on which the deflectors traveled are visible on the ground. (Source: The Rob Zone)
To my knowledge, these rails weren't used during the Space Transportation System (STS, aka Space Shuttle) era and the blast (aka exhaust plume) deflectors were since then permanently installed on the launch pad 39A.