You can change the GST rate of those affected GST code from 6% to 0% on the effective date that the Malaysia government scrapped off the GST. You should not amend the existing transactions once the rate has changed to prevent QuickBooks from recalculating the GST base on the new GST rate.
It is better to complete the transactions with 6% rated GST before amending the GST rate since QuickBooks does not have a change over date set in the GST profile.
As a QuickBooks administrator, you should lock the account by setting up a closing date and password to prevent other users from editing the existing transactions. Do a backup before the rate change, just in case you need to roll back after rate changed; and an integrity check (Rebuild and Verify Data) before and after rate changed.
For users who are using an older version of QuickBooks (especially Reckon QuickBooks version) may consider adding a new GST code than replacing the current rate. There is a risk that the old rate may get replaced when migrating to the latest version.