I noticed a few days ago when trying to setup a new ship that I am missing 5 epic phaser dual heavy cannons. It says they are equipped on a different ship but I can not find them. I checked my bank/account bank as well as all my alts and their banks and ships with no luck. I messaged support and was told to post it here by GM Ovric
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If you just click on your current ship, select a weapon or item catagory, it should also list all items on other ships as well. So that's another way to change items between ships, then just save a Loadout when you like the build you have. Depending where you are clicking an item can sometimes also display items in Bank as well as other ships.
Hope that helps you out a bit.