When using SQLite with EfCore under UWP, new SQLite databases are created in ApplicationData.Current.LocalFolder, in other words [user]\AppData\Local\Packages\[package number]\LocalState.

However, when I compiled my program as a packaged desktop app, the SQLite database was then created in [user]\AppData\Local\VirtualStore\Windows\SysWOW64. I am using WinUI 3 preview 4 with .NET 5 and VS 16.9.0 preview 4, and I created my app with the "Blank App, Packaged (WinUI in Desktop)" template that comes with the WinUI 3 preview 3 extension. I am creating my database using EnsureCreatedAsync() and I am using Microsoft.EntityFrameworkCore.Sqlite v5.0.3.

You may recall that #19754 and #19468 were earlier bugs in which EF did not initialize the SQLite directory. The workaround was to insert the following lines prior to using SQLite:

const int dataDirectoryType = 1;
const int tempDirectoryType = 2;
SQLitePCL.Batteries_V2.Init();
SQLitePCL.raw.sqlite3_win32_set_directory( dataDirectoryType, Windows.Storage.ApplicationData.Current.LocalFolder.Path);
SQLitePCL.raw.sqlite3_win32_set_directory( tempDirectoryType, Windows.Storage.ApplicationData.Current.TemporaryFolder.Path);

When I applied this workaround to my packaged desktop app, the SQLite database was then created in ApplicationData.Current.LocalFolder.

P.S. See also Eric Sink's entry in the SQLite repo