It can be made from whatever parts, new, used, doesn't matter.
The engine gets 'sealed' by the MotoGP's Technical Director.
It is then 'allocated' when it leaves the pit lane to go out on track.
At that time it's officially deducted from the allocation of 6.
I presume than an engine that grenades in the garage before going out, or on the first trip out on pit lane, wouldn't come out of the allocation.
A rider could start the 1st practice session of the year with 2 engines allocated, and get 4 more 'updated' units one-by-one during the season.
