Yep, sorry about that.
The game does only read from AI War 2\GameData\ModdableLogicDLLs during runtime. However, the extra copy in AI War 2\ReliableDLLStorage\ArcenDLLs is what is compiled-against. It would be how your external visual would be compiled against your regular external one. If you made a change that vis requires, then that would cause basically the main external to compile, but not vis. And that's probably what happened in your case.