@Dominik_Wosiek: Please note that Insync does not upload .gddoc, .gdsheet etc. files to your Google Drive. It seems that you moved/copied those .gddoc etc. files from Insync folder to the Google Drive sync folder?
Insync only creates those files locally as shortcuts to the corresponding Google format files.
Please send to us the logs.db and compressed copy of the dbs folder (present next to the logs.db file) at support@insynchq.com so that we could confirm how the deletions happened.