As far as the Charon bit goes, I noticed that if you exit the Charon system, save, than load that save and enter back into Charon, the Templar ship list will be randomized again.
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Edit: Forgot to post what I wanted to reply originally, have you tried jumping to a new system you've never been in before in that savegame, and seeing if your new items are being sold there?
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Standard operating procedure for me to change systems when testing scripts.