When you get in this state, try performing a Rebuild-All. If this fixes the problem, you may have the same issue I had.
Some background (my understanding):
SQLite has 1 managed assembly (System.Data.SQLite.dll) and several
platform specific assemblies (SQLite.Interop.dll). When installing
SQLite with Nuget, Nuget will add the platform specific assemblies to your project
(within several folders: \x86, \x64), and configures these
dlls to "Copy Always".
Upon load, the managed assembly will search for platform
specific assemblies inside the \x86 and \x64 folders. You can see
more on that here. The exception is this managed
assembly attempting to find the relevant (SQLite.Interop.dll) inside
these folders (and failing).
My Scenario:
I have 2 projects in my solution; a WPF app, and a class library. The WPF app references the class library, and the class library references SQLite (installed via Nuget).
The issue for me was when I modify only the WPF app, VS attempts to do a partial rebuild (realizing that the dependent dll hasn't changed). Somewhere in this process, VS cleans the content of the \x86 and \x64 folders (blowing away SQLite.Interop.dll). When I do a full Rebuild-All, VS copies the folders and their contents correctly.
My Solution:
To fix this, I ended up adding a Post-Build process using xcopy to force copying the \x86 and \x64 folders from the class library to my WPF project \bin directory.
Alternatively, you could do fancier things with the build configuration / output directories.