It could have "healed". I am a Flat Earther, but believe there is a dome (firmament) over the Earth. There are rumours of "sky-ice" in Antarctica comprising the dome, which needs to be studied only in Antarctica, as it is too cold to transport elsewhere for study (nothing can keep it cold enough to prevent it sublimating). Rumour is that it is much lighter than ice and sky-blue in colour, but it sublimates rather than melts. Apparently, when they have tried to drill through it with a tunneling machine, it slowly regenerates over days and weeks (the tunneling machine got stuck and subsequently entombed).
Assuming the above is true (a fairly big assumption), the sky ice dome could have been opened during the Great Flood, and the waters above poured into Earth. Over time, the sky-ice dome would have healed and closed again (at the conclusion of the 40 days).