This probably isn't the answer you want, but I'll give it a whirl...we're in a similar boat, although our course cycle is every two years. I create a course copy every year (so I have EL2008 in '08, EL2009 in '09, etc), which students then enroll and take. This gets us around the re-certification issue. Probably a lot of work for you, every 6 months, especially if you have many courses that all have that cycle.
In the future, I'll probably try working on a modification to address the issue of re-certification. I need to learn much more about Moodle's architecture first, though, as I have a feeling that the solution will need to reside in more than the certificate module.