I'm not entirely sure how the encounters that reward a special shadowrunner work from the rules. This is how I'm reading it.
You defeat an encounter that rewards a special shadowrunner of "+X". You set it aside in your play area, I guess wherever you're playing shadowrunners. At some point you can use this encounter as if it was a shadowrunner and it grants +X to a die roll.
Do you leave the die used to defeat the encounter locked on it or is this where the black dice included come in? If you use the locked die does it stay there till you use it even if it spills into the next player's turn?
It adds "+X" to any die roll when you use it and cannot be retained. Does it add "+X" to an existing roll or the die stored on it?
The die stays there until you resolve that column. Either by failing, scoring or Escalating it to a new column. Regardless of the outcome the card stays with the player and does not count against their shadowrunner limit of five.