I have several directories symlinked into the Insync folder and Insync correctly uploaded all the files contained in these folders. Today when I booted my PC I had no internet connection for a short while and since then Insync is going bonkers. It no longer detected one of the directories which contains around 4GB of data in more than 100.000 files, and just deleted them from Google Drive. When I restored them from the Google Drive web interface, Insync decided to download the whole directory again, this time with a (2) appended to the name. I’ve now tried several times to delete the directory while Insync is not running and then re-linking the directory or copying it over, to trick Insync into thinking it already has all the files downloaded, but no luck.
What it all comes down to is this: Insync does not see already existing files and directories and creates duplicates with a (2) appended to the name, regardless whether the files and directories are symlinked or copied into the Insync folder.