Huh.
Why can't you control the options to ebook-convert?
Are you using some sort of precompiled binary with an arbitrarily-canned cmdline which you don't have the source to?
Well, go ahead and write a batch/bash script that comes earlier in the PATH than ebook-convert, and your current process will find it instead. Make it add the debug flag to the cmdline and pass it on to the
real ebook-convert.