When users open a file from an online location (FTP or HTTP) using the Open from web button from the Open file dialog, Omniscope will open a direct stream to that file.
In order to let Omniscope save back to that location, you will need to tick Settings->Advanced->File settings->"Allow save to online locations" option and then save the file. This has been tested to work for files located on SharePoint document libraries.
Note: Omniscope will attempt to save back to the server via FTP or HTTP PUT.