This game have some problems.

[Freedom]

I didn't get heart squid and nugget in Water Lily den and Sea vent lab.
So I achieve to all item collection 100%... but Water Lily den entrance was blocked and Sea vent lab lay of the land had changed.
I'm set for the final boss... If I achive to 100%, will I reset...?

[Washing Machine]

Yeah, there's apparently a couple hearts and nuggets that you just get locked out of after the collapse. The game doesn't make it too clear either that that's a point of no return, and you can't make multiple save files during one run either.

I think I'm missing a statue or two too, and I've ran the entire map now spamming Seer everywhere, can't find all the secrets. 3 nuggets missing. Pretty sure the dungeons don't contain anything outside the 3 hearts each.

[Demajen]

There is no longer a lockout on nuggets. You can get any you missed from the scientists around the entrances to the missing area.

There's a map in the Guides section with everything marked on.

[Washing Machine]

Why you gotta do me like that, now I gotta recheck the entire map again.

Thanks I guess.

[Demajen]

If it's any consolation, on my first playthrough when I was trying to put the map together, I spent close to 5 hours looking for the final golden nugget for the last 1%.

[Freedom]

Originally posted by Demajen:

There is no longer a lockout on nuggets. You can get any you missed from the scientists around the entrances to the missing area.

There's a map in the Guides section with everything marked on.

Wait, scientist is around the entrance? I found one of scientist leading to water lily den entrance blocked, but he didn't give me anything... Where's other scientists?
And there's nothing map guide...

[TheForestSpirit]

Ugh I really dislike points of no return especially when they're not made clear. Very annoying to say the least.

[Demajen]

Originally posted by TaiwanNo.1:

Originally posted by Demajen:

There is no longer a lockout on nuggets. You can get any you missed from the scientists around the entrances to the missing area.

There's a map in the Guides section with everything marked on.

Wait, scientist is around the entrance? I found one of scientist leading to water lily den entrance blocked, but he didn't give me anything... Where's other scientists?
And there's nothing map guide...

If the scientists didn't give you anything, then you've already gotten the nugget they're linked to. The other two scientists are in Mossy Biome and Service Area, at the places where those zones originally linked up with Tour Route.

As for the missing heart squid, I don't know if you can get that any way, but I do know the game very deliberately railroads you past its cave in the "escape sequence" section.

https://steamcommunity.com/sharedfiles/filedetails/?id=2111608787 is the map!