hmm...don't really know what you mean... do you mean the fact that Belerinad was sunk? because actually the continent far to the east, known as the dark lands never changed or maybe you mean the fact that Arda was also rounded after the Downfall of Numenor.
Galadriel - Your answer is simple. Between every great confrontation between the Valar and Morgoth the world is changed, Here is a list of all the Big changes:
First war between Melkor and Valar - The great lake and the Ilse of Almaren have gine, replaced by Endor, Aman and the Gates of Morning.
War of Powers (second war) - the world is changed again. The inland sea of Ringol are gone and the Dark south land comes. Also a great gulf appears in ME.
War of Wrath (last war) - Beleriand mostly sinks underwater and the Realm of Morgoth destroyed. Mordor
Now comes Other changes:
End of the second Age - Eru sinks Numenor and the Inland sea of Helcar submerges.
these are all the pouints you list with a reason why next to each.
you forgot the most important change mouthofsauron the rounding of Arda when it was made round, like a sphere and that was also after the Downfall of Numenor
