I'm planning to migrate a managed Windows CE 6 application to run on Windows Embedded Compact 2013. Currently, the app is based on .net CF 3.5 and as you know, WEC2013 includes .net CF 3.9
My app uses a file based database (.sdf) and now I've read that .net CF 3.9 no longer supports SQL Server Compact.
Does this really mean that I have to switch over to SQLite or can I still include SQLCE in my cab file?
Yes, SQL Server Compact is no longer supported with Embedded Compact 2013, you can use sqlite instead https://cesqlite2013.codeplex.com/