Something to keep in mind first of all is that if you just want to debug your own plugin’s code it is not necessary to build Notepad++ yourself. What I do for my plugins is create a post-build event that copies my DLL into the Notepad++ directory and then runs the notepad++.exe as the application for debugging. I can then step through my code, etc.
In theory as long as the SciLexer.dll is next to notepad++.exe then it should work. The only thing I’d suggest is make sure you build them the same, e.g. 32bit/64bit/release/debug but it sounds like you are aware of the differences. I’ve always just stuck to 32bit without boost and haven’t had issues. If it is something specific to 64bit the maybe someone else can suggest some things to try.