SQL Tables aren't "Java" or "C#" - they are language independent and just exist within the SQL Server instance.
I'd start by using Google:
convert SQL server db to SQLite - Google Search[
^] - it shows a lot of routes to get from one DB system to the other.
Then it's down to your code: I wouldn't do a direct conversion of Java to C# because while that is possible, you don't necessarily end up with good code in the target language when you do a blind conversion between any two languages - and this is probably something you will need to modify and maintain for years to come, so it's worth getting the best starting code you can!
Instead, us eteh Java app as a template, a specification - and write new C# code to do the job properly using .NET instead of the Java framework.
Be aware that SQLite is just that: "Lite" - it doesn't contain all the features and facilities that "full fat" Sql Server does, and you will probably have to make significant changes if your java app uses anything "clever". For example, SQLite does not support stored procedures.
Also remember that SQLite is not and never will be a multiuser database: you will have horrible problems if you try!