If you start the event project under the Reputation tab, it will take the shards and, at least, reward Fleet Marks. That's what it did with my 15th shard after I already collected the rewards from the first 14 shards.
If you don't want Fleet Marks, then hold onto them and hope that the event comes back again and that they don't expire.
Please add Exploration to Star Trek Online! Are you sure it isn't time for a "colourful metaphor"? --Spock in 'The Voyage Home' Star Trek Battles Channel - Play STO more like Star Trek with challenge, teamwork and FUN!