I recently converted an mq4 indicator, and it worked perfectly.

I was just wondering whether there is a java intermediate source, or whether that is not available?

Is there an option on the compiler which will retain an intermediate java source for the converted mq4?

Could not find a java source output.

The latter.
No, this is done on purpose, because the used method signatures are subject to change, meaning that with every new release it is probable the java source code would need to get adjusted for the indicator/strategy to compile/work correctly.
If you are interested in method implementations, they are available at our public repository:
https://publicrepo.site.dukascopy.com/jforexlib/publicrepo/com/dukascopy/connector/MQL4Connector/2.7.7/MQL4Connector-2.7.7-sources.jar

Thank you, please fix that link as it appears to be broken.

It does work. Can you navigate the path manually https://publicrepo.site.dukascopy.com/jforexlib/publicrepo/? In any case the file is also available from your JForex-SDK project (locate it among Maven dependencies).