Hi Vedran,
Sorry for the delay in replying - our team has been all over the place with holiday vacations and travel, and we're still catching up! However, I checked with our team, and you figured out the correct solution! I would suggest that you reindex, clear the application cache, and restart PHP-FPM after adding the file to AtoM, for everything to show up correctly.
All the following assume an installation following our recommended instructions, and all commands should be run from AtoM's root installation directory (typically /usr/share/nginx/atom). They should also be run as the www-data user - if you have any problems with the commands, try adding sudo -u www-data before the commands to see if it helps.
Repopulate the search index:Clear the application cache:
Cheers,