I did this and had two primary orders glitch out. They were sitting complete in my inventory (yellow border), but the prompt to turn them in wouldn't come up when I talked to Banshee. Tried going to orbit, switching characters, resetting console, nothing. Ended up discarding them. 'Twas a bit butthurt.
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Yeah you need to watch it, sometimes it will allow you to purchase more then 5 orders resulting in the carry over weapons being bugged. Had this happen to me, just don't have more then 5 at a time