I'll get more into the question's details, but the reason I ask this is the Kensei Monk. Kensei monks cannot use Heavy weapons, which results in them being unable to use all Two-Handed weapons, but the Double-Bladed Scimitar is a two-handed weapon that is not heavy.
Since a Double Bladed Scimitar usually does 2d4 damage, if a level 5 monk replaced the die using Martial Arts to a d6, would the Double Scimitar change into 2d6 damage or 1d6 damage?
Best Answer
Martial Arts would replace the normal damage, if the weapon didn't have the special property
The monk's Martial Arts ability says (PHB, p. 78; emphasis mine):
The normal damage of a Double Bladed Scimitar is 2d4, which you can choose to replace with 1d4 (1d6, 1d8, or 1d10, as you level up) if you want. Or rather, you could, if the Double Bladed Scimitar did not have the special property (as V2Blast pointed out). Way of the Kensei allows you to use a weapon with the two-handed property, but still prevents you from using one that has the special property.
Putting the special property aside for a moment, each die you roll for damage from a weapon is referred to as a "weapon damage die". For example, the barbarian's Brutal Critical feature (PHB, p. 49; emphasis mine):
If Martial Arts was intended to apply to each weapon damage die individually, we could expect it to be worded something like this: