Do you mean 'missing from disk'?
IF so, you need to re-read (more carefully) how to upgrade a site:
https://docs.moodle.org/39/en/Upgrading
# 4 of 'Standard Install Package' ...
says:
"As mentioned above, if you had installed any plugins on your site you should add them to the new code tree (Moodle directory structure) now. It is important to check that you get the correct version for your new version of Moodle. Be particularly careful that you do not overwrite any code in the new version of Moodle and that you place the plugin folders in the correct directory (the same directory that they are in in the current installation.)"
Just like you had copied back into new code your config.php file.
If not above ... then please share exactly what that says.
'SoS', Ken