there is no runway 31L/R existing in real and therefore no terminal procedures (the sim can’t assign the existing terminal procedures to te current runways,). In the real world you have 14L/R and 32L/R …
In other words, the sim in outdated please report this to ASOBO.
normally the AIRAC Updates contains all Data and as you see in the charts app, we offer all data. But in MSFS we may not change the runway idents nor the runways itself.
So the MSFS AIRAC contains navigational facilities on airports like ILS, DMEs, GS antennas, terminal waypoints and NDB. Additional airways, enroute waypoints and navaids.
The question in your case is, why you have a wrong runway? Do you have a 3rd scenery installed for SKBO? I ask because Ian, our support manager, has tried the stock scenery and here he has seen the correct runway idents.