In El Capitan: Safari wiped the extension database?
I use OS X 10.9.5 (Mavericks) and I was preparing to ask: 


Where, on disk, does Tampermonkey for Safari store user data e.g. scripts?


Your question seems to answer my question!

(I had used fseventer to monitor file system activity whilst installing a script, but nothing conclusive was observed.)

In my case I assume that Tampermonkey dataloss resulted from an uninstall, followed by a reinstall, of various extensions. 

Background

Two sets of answers to frequently asked questions: 


http://tampermonkey.net/faq.php
https://forum.tampermonkey.net/viewtopic.php?f=16&amp;t=78


The Tampermonkey forum is limited, seeking Safari finds nothing: 


  The following words in your search query were ignored because they are too common words: safari …


http://tampermonkey.net/faq.php#Q106 explains how to export scripts, but I never imagined that losing (or removing) the database of extensions would also lose user data associated with any extension.