Try creating the following directory structure:
mydirectory
/com
/enterprisedt
/cryptix
/CryptixEDT.properties
placing your cryptix properties at the bottom level, as shown.
Then add mydirectory to your classpath before edtftpjpro.jar and run your app to see if it picks up your modified properties file. I believe it should as classes earlier in the classpath take precedence over classes later in the classpath. If that works then you can zip up mydirectory into mydirectory.zip, rename it to mydirectory.jar and place that in your classpath.