Might be a good idea to give a description of your hosting and setup. Only by looking at other post you've made do we see hints/clues ... in path of info shared on one posting seen is /client/ which is a clue there are multiple sites running on one server. So where you host, are you leasing a shared hosting solution/package?
We can see Linux clues (forward leaning slashes) and the fact you say 'killing processes' indicates command line access?
How did you upgrade? Does provider have a cPanel icon for upgrading your Moodle?
Conversion of assignments in moodle can be done in 2 ways ... unoconv (which involves python, minimal install of LibreOffice which is called by unoconv script in a headless mode, via a 'listener' which makes conversions from documents to PDF (if it can) one at a time for annotation/grading.
The other method of converting files is to use Google Document Conversion.
Which is your setup ... looks like unoconv to me from info shared so far.
In newer versions of Moodle, assignment setups have an option for restricting the type of file submitted. A * means any document type ... could restricted to .pdf, .doc, or .docx or ? upon submission. So do you have a course where students might have uploaded (no restriction) some file type that can't be converted to a PDF?
Also, is there any assignment made where students had to upload multiple files? Those would require the joining of the converted PDF's to show in one PDF in the grading/annotation area. That equals heavier processing.
In the setup of doc conversions, the moodle admin interface for that, does show what unoconv can convert as opposed to using Google. While unoconv has more, it can be problematic (such as you are experiencing) and less reliable than using Google.
Rather than shutting down .. put your Moodle in maintenance mode to keep students/treachers out. That will allow you to login as an admin level and work on stuff.
Suggest attempting to see what's in on of those tmp .pdf files
Sorry ... no quick fix! :|
Space ... one can, if there is anything in it, remove any/all files/folders in moodledata/trashdir/ manually. If cron isn't reaching it's clean up task that directory could contain lots of files no longer needed.