My question still stands, so I'll try to answer it for you. It is possible that in the last photograph, due to the location of the photographer, and the apparent breeze, that the Puerto Rican flag flipped over the American flag and is hidden by it.
But where is the American Flag in the first photo? You say its behind the Puerto Rican flag, even though it really isn't visible in any magnification of the original posted image, yellow line or not. Maybe it is, in which case both flags were present the entire time and our speculation is incorrect. But it isn't visible in the photograph, and if you look at the second photograph closely you will see that the two sticks the flags are mounted close together. And the fabric of both flags appear to be in contact. And the American flag is now on the entrance side of the pair of flags. And for it to change sides some force had to separate the fabric, which would be unlikely to be an aerodynamic force.
Or maybe it isn't there.
Apart from speculation, it really doesn't matter. If it is there then the photographs Sirius Lee's analysis relied upon happen to lead to an incorrect conclusion. That is a typical problem with any analysis of image data, which is why drone strikes guided by image sensors sometimes blow up a house full of kids.
And if the images showed the flags were changed during the day it would indicate that someone felt the need to do so, for whatever reasons they might have. Those reasons would be interesting to explore.
At this point perhaps the most interesting question is why is it such a big deal to you? You felt the need to make three images, even though one of them, the only one I asked about, really doesn't show the flag you say it does.