Is it safe to delete the /module folder?
Yes, you should be able to delete the versions of the modules directly under /modules, and clear cache; in theory that should be enough to get the system to re-register the same modules from their new locations.

Take a backup of the files and database first, and if you want to play it safe, delete one module folder at a time, running drush cr and checking that the version Drupal now sees is correct after each deletion.

It's probably wise to run drush updb after this, in case any of module versions have incremented and there are updates.