Add a "skill unslot" shard to the store for > 2500 but < 5000 trooper points (let's say 2750) that unslots a skill shard from a random skill. That way players have to choose to sacrifice trooper points that could have gone towards a new skill shard, in order to recover one at a slight "discount."
The trick would be adjusting Achievments (and possibly previously earned rewards) appropriately.