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Like Team Flare HQ in Geosenge Town, or Lusamine's room in Pokemon Sun/Moon.

Include places that don't actually change the name of the location your in, like Lusamine's room, but are still different areas.

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That link gives me the ss Anne, team magmaqua hideouts, and rooms in the Trick House
I do not know where I could find resources on this, you'd most likely need an answer from someone who's played every game (I haven't). But I can answer maybe two. Are we counting events, as well? I could give more in that case.

Mirage Tower (Emerald) will collapse once you reach the pinnacle  and select a fossil of either Lileep or Anorith. This one I speak from experience and know for a fact you can't go back to.

I also believe the Distortion World (Platinum) is impossible to return to. But don't hold that to me. I've never tried.

I know a lot more locations that *aren't* main series locations. (Gen 4 Mystery Dungeon games)
Marine Cave and Terra Cave become inaccessible after you catch or defeat the Pokemon inside it. The Distortion World has 2 parts, and 1 of them becomes inaccessible when you enter Sendoff Spring.
I don't need events, most of them you can't access later

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Mirage Tower (Emerald) will collapse once you reach the pinnacle and select a fossil of either Lileep or Anorith. This one I speak from experience and know for a fact you can't go back to.
I also believe the Distortion World (Platinum) is impossible to return to. But don't hold that to me. I've never tried.
commented Jul 26 by Ætherborn Rogue

Marine Cave and Terra Cave become inaccessible after you catch or defeat the Pokemon inside it. The Distortion World has 2 parts, and 1 of them becomes inaccessible when you enter Sendoff Spring.
commented Jul 26 by sumwun

  • Team Flare HQ
  • SS. Anne
  • Trick House puzzle rooms
  • Magma/Aqua Hideouts
  • N's Castle
  • Lusamine's room

Please comment if I missed any.

Source

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Your source doesn't work.
Btw the distortion world in Platinum can be accessed again. There is a portal inside of Turnback Cave.