Regardless of whether it is reissused or even where fare no longer exists, AA does have the details of the fare paid
The expectattion should be that you will receive credit as per the fare paid 5 miles per dollar spent
It does seem that AA has issues with some reissues and it may end up crediting as distance based, though would have expected it to be under the unknown fare earning rather than special fare earning
If the Travel Agent books directly with AA, it would not normally be a special fare , but a regular fare. If you purchased an economy ticket and upgraded using miles/SWU, the distance earning would be based on the underlying economy fare basis. If a business class ticket upgraded to 1st class, then would be based on the underlying business class basis
How much was the fare and what is the route?