Re-Keying in SQLite Encryption Extension

I have used SQLite Encryption Exchange for encrypting my database. I am trying to change the Key using PRAGMA rekey=.. I was able to rekey the database by executing the PRAGMA rekey=.. before activating the database and not otherwise. But I am unable to proceed with any other database queries. There comes an exception "Unsupported file format". The database can be opened using the new key externally. But not in my code.