Some of our users are getting an issue with the version of sqlite.interop.dll that is being loaded at runtime, and it\'s a real head scratcher.
Background: A WPF applica
We are dealing with this exact issue and the solution we found is to use the bundled package from the System.Data.SQlite website rather than the package from nuget: https://system.data.sqlite.org/index.html/doc/trunk/www/downloads.wiki
The bundled dll has both the managed and unmanaged assemblies merged so there is no need for dynamically loading the correct Sqlite.Interop.dll so you don't have the issue of conflicting versions in the appdomain.
When using the bundled assembly you need to include your own logic in your application's installer to decide which dll to copy (x86 or x64).
We haven't had any more issues with conflicting versions since using the bundled assembly.