Sorry, I do not know anything about Business Central.
But if you are still getting "Could not load file or assembly 'System.Threading.AccessControl", then if means Business Central is somehow still loading .NET framework version of the assembly from somewhere. Doesn't the error message (or some logs) include path to the assembly that is being loaded? Try to search whole system for any WinSCPnet.dll files.

Hello, I upgraded an older BC Version to BC25 and in a function I now get the issue:

A call to WinSCP.Session.Open failed with this message: Could not load file or assembly 'System.Threading.AccessControl, Version=0.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a'. The system cannot find the file specified.

I found a thread here but I'm not good with understanding what I'm supposed to do.
assembly 'System.Threading.AccessControl issue on Business Central v22.0

I copied the WinSCP Addin Folder from the old server to the new one but it didn't fix the issue. I tried downloading the current WinSCP dll from here:
https://winscp.net/eng/downloads.php
(.NET assembly/COM library)
and dragged the new version in the netstandard2.0 folder into the addin folder but that didn't fix it either.

Does anyone have an idea?