Hi Tatiana,
Did you remember to clear your browser cache as well? It's possible it's only your web browser showing you an out-of-date version of the page. If that doesn't work, remember that PHP-FPM has a cache as well, as does memcached - be sure to restart all three! On Ubuntu 16.04:
- php symfony cc
- sudo systemctl restart php7.0-fpm
- sudo systemctl restart memcached
- (then clear your web browser cache)
If you want to double-check that the correct logo is in place, you could also go an manually verify it in the uploads directory. The uploads directory is consistently organized like so:
/usr/share/nginx/atom
└── uploads
└── r
└── institution-01
└── institution-02
└── institution-03
└── conf
└── logo.png
That is, in the uploads directory, all subdirs are nested in an r directory, after which further subdirectories use the name of the institution. The repository logo is always placed in a further subdirectory of the institution's subdir, called conf.
You can always navigate there to double-check that the correct file is now located there, and the previous file has been deleted / overwritten. Here's an example of the organization as seen in my Windows Explorer, using the Vagrant box and our public demo data:

For further details on the organization of the uploads directory, see this previous post: