Disabling the vanilla stronghold but not adding the Lost Castle to the eye_of_ender_located structure tag means Eyes of Ender will no longer be able to find anything
https://github.com/misode/mcmeta/blob/data-json/data/minecraft/tags/worldgen/structure/eye_of_ender_located.json

Simply add your structure to this tag and the eyes should be able to find your castle and prevent players from being confused

A player came to me thinking it was Repurposed Structures breaking the eyes but turns out, it was Lost Castle on 1.20.1 Forge.

The Lost Castle - Location NBT Fix - 1.0.0.zip Came across this issue today, and looks like it may be being ignored... so I wrote a datapack to fix the issue myself! Hopefully it linked to this comment correctly and anyone who visits here looking for an answer will find what they're looking for.

Honestly with a fix this simple you could probably submit it as a pull request. If you don't want to go through that process, do you mind if I do it in your stead?

@TelepathicGrunt thanks for reporting my issue. I have a game running under 1.20.1 Froge and tlc_forge-1.0.3-R-1.20.X. When an eye of ender is thrown nothing happens, inventory count doesn't drop.

The Lost Castle - Location NBT Fix - 1.0.0.zip
Came across this issue today, and looks like it may be being ignored... so I wrote a datapack to fix the issue myself! Hopefully it linked to this comment correctly and anyone who visits here looking for an answer will find what they're looking for.