But Thutmose III did have her name scratched out of inscriptions.
Perhaps, but that’s just as easily explained as being something that’s been taught and accepted, since AFAIK there aren’t any ancient accounts of his having done that. Each new pharaoh was (at least supposed to be) born of the same line as the previous pharaoh, hence all the ceremonial marriages. Hatshepsut was officially the wife of her own father, brother, and nephew in succession.
Centuries later, the Ptolemaic dynasty actually did carry out brother-sister marriages and reproduction. In earlier dynasties there were consanguineous marriages with cousins and whatnot, and apparently the formalities were spun to make it possible for a pharaoh to choose his successor based on actual abilities. As the Seti character said in 1956’s “The Ten Commandments”, he owes that to his fathers not to his sons.
OTOH, Hatshepsut’s daughter was literally of the same womb (matrilinear succession), and Hatshepsut’s personal campaign of rebranding appears to have been to set up her daughter as her own successor. It’s difficult not to see Senenmut’s hand in all of the intrigue. Assuming that he didn’t die of natural causes, I’d imagine he was killed off at T-III’s earliest convenience.
The Red Chapel was unfinished at H’s death, and was finished by T-III, but later demolished and parts of it used to construct other structures at Karnak, including some of T-III’s renovations. ( https://digitalkarnak.ucsc.edu/red-chapel/ )
Repurposing earlier works was common, right back into the Old Kingdom, there are examples at Giza. Ramses II had King Tut’s major construction of the Colonnade of the Temple of Luxor recarved with his own name. The reason the actual history is known is that Tut’s cartouches in the darkness near the ceiling were either missed or deliberately skipped. Ramses II may not have even known, or considered it unnecessary because it wasn’t readable from the floor. A colossal head of one of the pharaohs Sesostris was recarved as Ramses because there was a facial resemblance. The original headdress style on the sides of the face can still be seen, while the upper part was completely recarved.
https://www.britannica.com/biography/Hatshepsut
...following her death, Thutmose III ruled Egypt alone for 33 years. At the end of his reign, an attempt was made to remove all traces of Hatshepsut’s rule. Her statues were torn down, her monuments were defaced, and her name was removed from the official king list. Early scholars interpreted this as an act of vengeance, but it seems that Thutmose was ensuring that the succession would run from Thutmose I through Thutmose II to Thutmose III without female interruption. Hatshepsut sank into obscurity until 1822, when the decoding of hieroglyphic script allowed archaeologists to read the Dayr al-Baḥrī inscriptions. Initially the discrepancy between the female name and the male image caused confusion, but today the Thutmoside succession is well understood.