I think there is a slight difference here and you should be okay.
The landlord will have been entitled to a six month free period because it was empty.
You can have six months free in any twelve month period.
You are now asking for an exemption because the property is uninhabitable.
The first exemption should have no bearing on the second.
And as the new council tax year starts in April you can argue the new twelve month period starting from then anyway.
I always through Feb and March were free effectively, if you paid for the twelve months over ten etc?
Have you checked the exact wording of your Council's terms?