Considering the files were not uploaded via media uploader, they are present in the server but there's no reference to them in your database (in a little more detail).
In order to fix it, install the Media Sync plugin. Once it's active, under Media > Media Sync > Scan Files and select the files you want to import by click the checkbox next to them. Make sure also you untick the selectbox Dry Run (test without making database changes).
Then, when the time comes for you to be ready, just click "Import Selected" and you should see something like this
Once it is finished, you can visit Media > Library and you'll see all your imported files there.