I am using latest version of Sublime Text build 3143 and Ubuntu 17.10 with gnome 3.26.1
When I save files with authorization pop-ups some new lines get added to the file, I have checked the files has been saved with my contents but in the UI it’s adding some new line.
Try reverting Sublime Text to clean state: https://www.sublimetext.com/docs/3/revert.html, perhaps there is some package inserting these lines?
Are you using some package as remote FTP access or these files are accessed locally? If the files are remove, it should be a bug on the package which you are using for the accessing them. Then you can open a issue on the package which you are using for remote file access.
