So , it seems to me that you don't have tikz in your minimals anymore. Can you try to re-install?
Ah -- sorry, bad english. As Thomas wrote, pgf is not part of minimals . Try to reinstall pgf from ctan; if you can, it's better to make a symbolic link this time.
Or you can try to see if there are some options of rsync to preserve your files, but eventually you can end in messy and unusable minimals.
The idea of minimals is :" the minimum complete for a project"
and is good to have multiple minimals. Actually I have *) current -- reinstalled 2~3 times at year *) beta -- can be reinstalled 2~3 time at week *) beta-lunatic -- my project, frozen *) beta-pdflualatex -- another experiment, not frozen
and a couple of current in production. In you situation should say to make a beta-pgf To update 1) make a new minimals called beta-pfg-new 2) copy into it rilevant files and setup from beta-pgf 3) test beta-pdf-new
4) When tests are ok, store beta-pgf in another location and rename beta-pgf-new in beta-pgf