I think it's important to get the terms straight to avoid confusion. E.g. the rulebook says the following about ninja Markers when a Ronin in defeated:
Once there is no free space on a Ronin TileThe Attacker's Reserves starts with 40 Ninja Markers, and the remaining 10 Ninja Markers go to the Ninja Pool.
to place Wounds (Ninja Markers), a given
ronin is eliminated. The Defender removes
all Ninja Markers from his Ronin Tile and
returns them to the Ninja Pool – not to
the Attacker’s Reserves!
There isn't any way for Ninja Markers to go anywhere else. They're either returned to the Ninja Pool or the Attacker's Reserves.