Line an 8-inch square pan with parchment, leaving overhang. Lightly coat the parchment.
Drain the cherries, chop them, and blot thoroughly until dry to prevent watery fudge.
Warm chocolate chips, condensed milk, and butter in a saucepan over low heat, stirring until smooth.
Remove from heat. Stir in vanilla, fine sea salt, and almond extract if using.
Fold in the chopped cherries and dark chocolate flakes until just combined.
Spread the fudge into the prepared pan and smooth the top with an offset spatula.
Sprinkle mini chocolate chips and flaky salt on top, pressing lightly so they adhere.
Chill until firm, about 2 hours. Lift out by the parchment and cut into small squares.