Not sure if this would even work, but you could try adding qualis gems to the inventories of units specific to the lair instance, like the leader enemy types, which should give you a small chance to loot one.
You could also add a minority enemy spawn to that party template so as to induce a relatively low drop chance, as giving gems to frequently occurring units could make them too abundant. You might even need to adjust the (Abundance) value for the Gem itself to achieve the best balance.
This is an untested theory, but it might work.