It sounds like your GST Tax Item is linked to another Tax Code. Check each tax code you have for GST collection and see which Tax Items they are linked to.
Are you able to use the existing Tax Code linked to Tax Item GST for your Sales?
If not, create a new Tax Code and link it to the GST Tax Item.
We didn't have any Tax Items linked to any Tax Codes in our system. We set up new Tax Items in system, however it is not allowing us to make these changes saying "This Tax Code has been used, you cannot change it unless you change all transactions, items, accounts, customers and suppliers associated with it". Now we have deleted tax invoice (we only had one completed), Deleted customer & supplier (only entered 1 of each), Checked in Reports of our Profit & Loss and there are no transactions whatsoever, so not sure why it's not letting us save the changes for GST TAX CODE?