The precise claim is still quite vague to me. What exactly is meant by "Hindu ancestry"? It isn't like there is some specific Hindu gene we can test for, as far as I can tell. If the details are spelled out anywhere in the linked resources, I'm not seeing it.
That said, there is some relevant genetic research. In particular I would point to "Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations", published in Nature, 2009. The key conclusion:
Overall, our results support a model according to which the spread of Islam in India was predominantly cultural conversion associated with minor but still detectable levels of gene flow from outside, primarily from Iran and Central Asia, rather than directly from the Arabian Peninsula.
Older studies I'm seeing like this of specific Muslim populations within India seem to support the same conclusion.
So all this really tells us is that on the one hand, the population of the Indian subcontinent shares a lot of common ancestry, but on the other, Muslim populations may also share some distinct patterns of ancestry unto themselves. This is relevant context for the claims you are asking about, but I would emphasize that the claim as stated in the question is perhaps more vague than wrong. Just one key question that would need to be clarified is at what point in history do certain genes become "Hindu genes", if any such concept even makes sense at all? The links you provide don't seem to address this.