Q:

How does the dispel check work for single-target spells becoming multi-target using higher levels?

The 2nd level spell Hold Person can affect multiple targets when upcast with a higher level slot.
Suppose a wizard uses a 6th level slot and successfully holds 5 humanoid king's guards with the spell.
The Dispel Magic spell simply works automatically if it targets any spell 3rd level and below. The caster needs to make an ability check to ends spells of a higher level with a DC of 10+spell level.
If the king's adviser wished to dispel the spell on one of the guards, would a check be unnecessary because he is attempting to end a 2nd level spell that affects multiple targets or does he need to attempt a DC16 ability check?

A:

When a spellcaster casts a spell using a slot that is of a higher
  level than the spell, the spell assumes the higher level for that
  casting. (PHB 201)

So it has to be dispelled as a 6th level spell if it was cast using a 6th level slot, regardless of the "basic" level of the spell.

