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If you have a mage handy he can create a new rune for you. Otherwise you can go to a harbor master and request a new rune.
Putting your ship run in a rune book or atlas is a good idea for several reasons.It does not take up a separate storage slot in your backpack.You do not need to insure the rune because rune books and atlases are blessedYou don't loose the rune while crafting rune books and atlas due to a bug that considers ship runes as unmarked and uses them during the crafting process.