First, check file permissions and make sure Plex Media Server can access the files.
With DSM 7, Plex Media Server runs under the system internal user PlexMediaServer. This is a change from DSM 6, when the username was plex.
See FAQ 29 - DSM 7 - Give PlexMediaServer access to your media. It shows how to give user PlexMediaServer access to your media files.
Second, you can configure Plex to scan your libraries automatically if it detects any changes and to scan at a preset interval.
Go to Settings → Library + Show Advanced.
Look at the first four options.
Info on all the options is at Plex Docs → Server Settings → Library.
Third, you can always manually scan the libraries.
To scan an individual library, using Plex Web or Plex Desktop, mouse over the library name. Select the three vertical dots, then choose Scan Library Files. See screenshot below.
To scan all libraries, select More >, then mouse over your server name. You’ll see the same three dots and an option to scan libraries, except this scans all libraries on the server.
You can also go to Settings → Libraries. You’ll see a list of all libraries on your server. Above the list of libraries is a Scan Library Files button. This will also scan all libraries on the server.
