An override die is a trick a DM can use to bend an existing random table or procedure in order to favor a particular result. By using an override die, the DM can avoid needing to make a new random table for the particular scenario.
Examples
A DM uses the random encounter tables in Appendix C, but always rolls a d10 along with the percentile dice. If the d10 shows a 1, the DM places a homebrew monster instead of the monster shown on the percentile dice.
A DM uses the standard alignment chances mentioned in the henchmen generation rules, but rolls a d6 along with them. If the d6 shows a 1 or 2, the rolled alignment is ignored in favor of the prevailing alignment of the settlement.
An example straight from the rules: Magic items are rolled for with percentile dice, but a d10 is rolled along with them. If the d10 shows a 1, a treasure map is placed instead.
A DM uses Appendix B to generate terrain types, but rolls a d6 along with it. On a 1-3, the rolled terrain type is replaced with the dominant terrain type of the region.