If clear fuel is dumped in a dyed fuel tank is there an allowance that can be taken to get the tax back?

Possibly. You should file a claim for refund as follows:

Complete a Form R-20127, Claim for Refund of Taxes Paid, which can be downloaded from the Department of Revenue website;
Attach a notarized statement certifying that the tax was paid on the clear fuel at the time purchased; and
Attach a copy of the invoice showing the number of gallons being claimed and a statement attesting to the facts.

After the facts and documents supporting the claim for refund are filed and reviewed, the taxpayer will be notified of the Department’s decision.