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I'm asking about Pokemon that appear as part of "in-game events" instead of random encounters, disappear when the player runs from them, and don't reappear every week, like BW Foonguss and XY Snorlax. I'm asking about every game from Pt onward. Please don't question my curiosity.

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All of these Pokemon reappear if you run OR if they faint, right? What about the Pokemon that are not in this answer? Do they disappear forever or something?
All of the Legendaries reappear except the Lake Trio in Gen 4.
The only non legendary interactable Pokemon left that I can think of is Foongus/Amoongus and I'm pretty sure they don't respawn but I don't have a source
What are the other non legendary interactable pokemon
stuff like Pt Rotom and BW Musharna. I think this is the full list: https://bulbapedia.bulbagarden.net/wiki/List_of_wild_Pokémon_from_in-game_events

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In any game prior to Pokémon Platinum, most of these Pokémon are permanently missable. If the player defeats any of them, that Pokémon will not appear again.
The exceptions are Spiritomb in Diamond and Pearl and these time-based Pokémon: Lapras appears every Friday on Pokémon Gold, Silver, and Crystal (and their remakes), and Drifloon also appears every Friday, in Diamond and Pearl as well as Platinum.

That takes out a large portion of our Pokemon. However this is only if you defeat the Pokemon. If you run from any in game event Pokemon in Gen 1 or 2, than it will disappear forever. In Gen 3 and DP, legendary Pokemon will respawn if you ran away or defeated it, (with the exception of Azelf and Uxie in DP,) however other Pokemon will become unavailable. In Platinum onward all in game event Pokemon will respawn after entering the Hall of Fame if defeated or ran from.

Rotom in Platinum respawns after HoF-(research)
Musharna respawns the following Friday (research)
I couldn't find anything on the BW Zoroark but you can't really get that event anymore unless you still have the Shiny Beast unused in your boxes.
Volcarona respawns (experience)
Nature Preserve Haxorus immediately respawns if ran from (a lot of research)
HA Jellicent, Braviary, and Mandibuzz respawn every week (research)
XY snorlax respawns after HoF (experience)
ORAS Kecleon respawns immediately after running (experience)
Alolan Exeggutor respawns immediately
Ultra Beasts in SM respawn immediately and in USUM have to be found again (experience)
Galarian Slowpoke respawns immediately(experience)
Non Dynamax Adventures legendaries in SwSh respawn immediately (experience) except the birds which in that case you have to fast travel for them to appear again.
SwSh Spiritomb you have to interact with 32 people again. (Research)

Additionally, there are Voltorb, Electrode, Foongus, and Amoonguss disguised as items in some games. They don't respawn if they are defeated

In Pokémon Diamond and Pearl, all of these Pokémon are permanently missable if the player defeats them, except for Drifloon, which appears every Friday after Mars was defeated for the first time, and Spiritomb, which appears every time the player uses an Odd Keystone and greets 32 players in the Underground. Starting from Platinum, the Pokémon respawn if the player defeats them and then defeats Cynthia, and therefore are not permanently missable anymore.

Source

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Again, this article only says they'll respawn if you defeat them. Are you sure the same thing happens if you run from them?
In Gen 1 and 2, if you run from an interactive Pokemon it will disappear forever. In Gen 3 and Diamond and Pearl if your run from an interactive legendary pokemon it will stick around but the Pokemon will not stick around if it is not legendary. Any game after DP if you run from an interactive Pokemon then it will either immediately reappear or appear after you enter the Hall of fame
How do you know this?
In Generations I and II, if the player runs from any of these Pokémon, it becomes permanently unavailable

Starting in Generation III, if the player runs from a Legendary Pokémon, the Pokémon respawns, but other Pokémon still become permanently unavailable. Starting in Pokémon Platinum, if the player defeats an in-game event Pokémon, then it respawns next time the player enters the Hall of Fame.

Starting from Platinum, the Pokémon respawn if the player defeats them and then defeats Cynthia, and therefore are not permanently missable anymore.

That was all copied from the article. I understand what you are saying that the article does not explicitly say that any Pokemon after Platinum will respawn if you run from it. However I do know that every single legendary will after entering the Hall of Fame at the very most, so I went and either did research or checked myself the rest of the non legendaries I wasn't sure about.

Rotom in Platinum respawns after HoF-(research)
Musharna respawns the following Friday (research)
I couldn't find anything on the BW Zoroark but you can't really get that event anymore unless you still have the Shiny Beast unused in your boxes.
Volcarona respawns (experience)
Nature Preserve Haxorus immediately respawns if ran from (a lot of research)
HA Jellicent, Braviary, and Mandibuzz respawn every week (research)
XY snorlax respawns after HoF (experience)
ORAS Kecleon respawns immediately after running (experience)
Alolan Exeggutor respawns immediately
Ultra Beasts in SM respawn immediately and in USUM have to be found again(experience)
Galatians Slowpoke respawns immediately(experience)
Non Dynamax Adventures legendaries in SwSh respawn immediately(experience)
SwSh Spiritomb you have to interact with 32 people again. (Research)

No joke I got the Google Chrome search contest 2020 scam while researching. Most of the research was on Bulbapedia.

I can add this to my answer if you'd like
If you use information from a website in your answer, you need to link to where you got it from. I don't know about the rest of the users here, but I personally don't really trust people when they say "I researched this to get the answer" or "I found it on [website]" but fail to provide any links to their sources, and I'm pretty sure that sumwun feels the same way about this.
What about Foongus in the Unova games?
Foongus disappears forever source experience