Is there a way to annotate a check to properly indicate that the debt is not acknowledged, but being disputed?
Not really, under the Fair Credit Reporting Act and the Fair Debt Collections Practices Act, if you dispute a debt, the owner of that debt needs to provide evidence that the debt is in fact owed. Any reports to the credit bureau needs to reflect that it is disputed. Contesting the debt with whomever you are paying it, is the proper way to handle this, not with check annotations.
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