Wash and thoroughly drain the cherries. Pit them over a bowl, collecting both the pitted cherries and the juice. Strain the cherry stones and juice through a sieve, draining the liquid back over the pitted cherries.
Zest the lemon using a zester or microplane; if you don't have one, peel the skin thinly and cut into fine strips. Squeeze the lemon to extract the juice.
In a large bowl, combine the pitted cherries, lemon juice, lemon zest, and brown rock sugar. Cover the bowl and place in a cool location (not the refrigerator) for 8-12 hours overnight.
The next day, cut each vanilla pod in half lengthwise. Cut the whole pods into 2 pieces and the halves into 1 piece each. Place 2 pieces of vanilla pod into each prepared jar.
Stir the cherry mixture thoroughly (most of the rock sugar will have dissolved). Distribute the mixture evenly among the jars.
In a separate container, mix the amaretto and rum together. Pour the mixture over the cherries in the jars to fill them. If needed, add more amaretto and rum in equal proportions.
Seal the jars tightly. Place them in a cool, dark location and let them steep for at least 6 weeks, preferably for 3 months.
Store in a cool, dark place. The preserved cherries will keep for at least 1 year.
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