Replacing file deletes root folder of the path to it relative to LocationId

[ZeeWanderer]

Bug Report

Summary

Since transitioning to Library Items when replacing an existing file Apply nukes the folder structure. Granted I only manage Pacific Drive with the App support for which is in my fork, #1747 so it's entirely possible my own code is at fault.

{Game} is H:\SteamLibrary\steamapps\common\Pacific Drive, {GameMainUE} is H:\SteamLibrary\steamapps\common\Pacific Drive\PenDriverPro, and the file game path is {GameMainUE}\Plugins\DLSS\Binaries\ThirdParty\Win64\nvngx_dlss.dll. I have gone over action groupings, and that part works as expected: the file gets backed up, deleted (just the file), then the new file gets extracted and then at some later step the entire relative root of the path to it gets nuked ({GameMainUE}\Plugins).

Steps to reproduce

Manage Pacific Drive
Add dlss DLL zip to library as From Drive.
Enable the "mod"
Apply it
{GameMainUE}\Plugins disappears entirely

What is the expected behaviour?

dll gets replaced with a new one

Other information

Diff appears to be correct:

Unmanaging the game only puts back the backed up dll that was replaced, all the other files in Plugins remain gone.
nexusmods.app.main.current.log