The pdf documents created by the certificate module in Moodle2.0/2.1 are stored in moodledata/filedir folder only if the certificate instance has the "Save certificates" option checked.
Unfortunately you have no means to clean these documents yourself because it's quite impossible to retreive them as the folder hierarchy under moodledata/filedir has non human readable subfolder and files names.
But the place where the pdf certificate is stored is known from the certificate module so I don't think that upgrading to the https://github.com/PukunuiAustralia/moodle-mod_certificate version will cause any problem.
In any case it would be best if the teacher has an option to "regenerate" all the pdf documents stored by an instance of the certificate module (for instance if the teacher wants to change a graphic element of the certificate and wants to update all issued certificates), but currently to my best knowledge, that option doesn't exist.
A workaround I have used is to uncheck the "Save certificates" option, but of course that means that certificates will be reissued each time a student request to view his/her certificate.