It messes up the tilesets, switching around tile position while retaining initial colliders, at random, and by consequence, the scene tilemaps also get messed up.
Amazingly, this happens gradually after a few seconds, as if there is some indexing going on in the background during which tiles are wrongly attributed and then replaced.
Re-installing 2020.1.16 and opening the project in this version solved the problem (just as well, or this would have been the final straw the week the project is off to console CERT)