Are they supposed to just become a card in your inventory or just disappear forever?
Because my Romulan had the officer you get from siding with the feds just become a card, while the one I was supposed to get for rescuing the republic ship from Cardassians just vanished. So what exactly is supposed to happen, was the fed officer just a special case? Or do i need to send in a support ticket about this?
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Most people pick 4 to use all the time and then train them up with skills and give them the best ground equipment, but no one is forcing you to do that.
Your extra boffs can be sold on the exchange (except some special ones) or turned into training manuals.
Your "missing" boffs might be under Stations at the bottom of the page. Not all unused boffs go into your main inventory.
If you want more boffs on your active list, you can buy extra slots from the C-Store but there is no real reason to have more than (at most) space team + ground team.
Clicking "Not Yet", puts the Boff into your "Candidate List". The button for that list is in the Stations tab of the Player Character / Bridge Office status window; it may not state "Candidate List" and I cannot verify at the moment. Regardless, the "Candidate List" can store 12 Boffs if I am not mistaken. If there are currently 12 Boff candidates on that list, then the Boff will be placed in your Personal Inventory. If your Personal Inventory is full and you do not see your Boff, then you should see a button called "Overflow Bag", that would be the final place to search for a Boff.
This is a viable option if they are holding inventory space, which is smaller when you start out ( well it stay small till you buy more slots, but when you get zen you will most likely expand inventory and bank once each unless you like to transfer gear between alts, alot.)