I don't know if SQLite is available on Windows but it allows SQL queries and can be used as an embedded database. In contrast to mSQL it is still actively supported. (unless that has changed via another package using the same letters or mSQL being developed again since last I looked).
More generally, since it's SQL if you are careful to use only widely supported SQL syntax, then it should be easy to port the application to use a traditional RDBMS ( Oracle, Sybase, PostgreSQL, MySQL etc )
There is a DBD::SQLite module on the CPAN.