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Depending what you have enabled as far as what contributes to the shipping rate (weight, sub-total, quantity, etc), change the conditions so that a rate would be impossible to match. For example, if there is a weight range of 5-25, change it to 50000-250000. Since this row will now never be seen by the customer, you can also change the description by adding "(added 000)" to remind you what the original range was.

I tried to look for this on the other day and I couldn't find a way to disable it apart from deleting a row. So make a note of what it is and then delete it. When you're ready to offer it again, re-add the row. In fact, I had the need to do this now and then, I will raise as Feature Suggestion for this. Edit - I have raised this - https://github.com/cubecart/v6/issues/2832