If you read the document again (?) maybe you'll see it's not about proving a negative. Instead, it's a standard of due care. Did you check whether using some particular tool illegally discriminates and document that consideration? From the document itself:

"Clarifies that, when designing or choosing technological tools, employers must consider how their tools could impact different disabilities;

Explains employers’ obligations under the ADA when using algorithmic decision-making tools, including when an employer must provide a reasonable accommodation;"

If it's a civil case, it's just the preponderance of the evidence. The jury just has to decide who they think is more likely to be correct.