Most 3rd party applications use the sqlite3.dll file, which you can easily just replace. As a matter of fact, you can make a copy of System.Data.SQLite.DLL and rename it to "sqlite3.dll" and all those 3rd party utilities that use the sqlite3.dll will run against it just fine.
If you need to create a database using an older file format, you can use the legacy_file_format pragma after opening the connection. To do it, just do this right after opening the connection:
using (SQLiteCommand cmd = new SQLiteCommand("PRAGMA legacy_file_format=1", connection))
{
cmd.ExecuteNonQuery();
}
This will make SQLite use the 3.0.0 file format which will be upward compatible with all newer 3.x libraries. Here's a list of the versions that have caused a change to the file format:
** file_format==1 Version 3.0.0.
** file_format==2 Version 3.1.3. // ALTER TABLE ADD COLUMN
** file_format==3 Version 3.1.4. // ditto but with non-NULL defaults
** file_format==4 Version 3.3.0. // DESC indices. Boolean constants
Robert