How to check and fix redundant vias in Allegro X APD?

There is an easy check to identify and fix your duplicate vias that are the same XY location.

You can utilize Package Design Integrity Checks in Packaging tools. If you have not looked into the below post yet, please have a look:

Package Design Integrity Checks

In order to perform the checking, you have to specify a tolerance value for the “packinteg_redundant_via_tol” environment variable from Setup > User Preferences in the Ic_packaging/Package_integrity folder. For example, a tolerance value of 1um is set in the following image:

Once this is set, enable "Redundant Padstacks" checking from Tools > Package Design Integrity in the Manufacturing folder and click Apply.

You will get the violation coordinate as well as it adds external DRC.

A small tip, If you want to remove the duplicate via when running the Package Design Integrity Checks, then enable the option 'Fix errors automatically (where possible)