Well, I can tell you that although many people say this for generations, at least with the records that i've gone through and I know other Filipinos who traced their lineage in other places not where I'm tracing, they were able to trace their ancestry without any problems.
However, I don't know if these so called records were limited to the recent years? Or specifically to a small area where they occupied. Say that they only occupied Manila, a very small handful obviously. Did they have enough control to order records throughout the entire archipelago to be destroyed? Did they try that? I can only tell you from experience that many of us have had no problems tracing.
But since you put it that way specifically where a family member was killed and relatives, male relatives too (similar to a friend's story I heard) plus his house was burned, I am guessing that this is how the story is perpetuated inaccurately. That's just my assumption, since I always tell people that it isn't true that records were burned. Because in reality, there are many records still in tact.
Also, I find most people who say that actually never tried to trace their ancestry. So unless you have actually traced ancestry using church records, and I know a distant cousin who is commissioned by the city govt. where our family is from to do actual research, and has presented electronic copies of writings from the 1800s just as I have copies from the 1920s and further back with the bulk of my copies in the 1860s & 1870s, that traces my own ancestors who lived in the mid to late 1700s, I'd say that the records are not burned.
And the story I heard growing up was that churches were burned. Perhaps a few were. But doesn't mean all churches and records were burned. Another example would be my grandfather's ancestry. He was from a very tiny island and when I went there, there were a few churches actually, but when they were built, I do not know. However, prior to going to that island, we were on another neighboring island, larger and where my grandfather was from was a municipality of the larger island, so anything with the govt. was handled there. And it was there in the main town's church I was able to access recs. of the people from that island. So what I'm saying is that sometimes, at least in my grandfather's case, one church holds records of another parishes/areas.