Migrating SQL server compact 3.5 to Sqlite

Hi,
We are migrating our operating system from WEC7 to WEC2013, and as part of that migration, we are moving our database from SQL Server compact to SQlite.
What is the best way to upgrade the customer database in the field without losing data? Please share your experience if you have one.
Part of my research I found that ExportSqlCe.exe (thanks to ErikEj) can be used to export your database schema and data, later using sqlite3.exe to create Sqlite database by importing the file exported. This would not solve my problem as these tools are developed to run on regular .Net framework runtime. However we need these tools to run on .net Compact Framework runtime.
Regards,
Srikanth