Did you use the same external drive folder with Insync app on another machine? If so, please note that this is not supported. Each Insync app instance should have their own separate/exclusive Insync folders - must not be used with Google app or another Insync app instance.
Did you unselect the files that you speak of, under selective sync settings? If so, please note that that's the expected behaviour. When you unselect the files, Insync deletes them from the local Insync folder but the files are kept intact on Google Drive web. Are the files present on Google Drive web?
Insync never deletes users' files on its own. Further, it only trashes the files on Google Drive web when you delete them locally. Similarly, when you remove a file from Google Drive web, Insync puts the corresponding file (if it was being sync'd locally) in the .insync-trash folder for 30 days before permanently deleting it.
Re: Conflict control - the local version of the file always takes precedence and overwrites the remote file as a new version so that no data is lost. You can revert to the previous version or extract data from the previous version on Google Drive web by going to File -> Manage versions.
As to Process Kill Routine, Insync does provide the quit functionality: Right click the tray icon -> Quit. Does it not work for you?
Please send to us the logs and compressed copy of the dbs folder (present inside the same location as that of logs) at firstname.lastname@example.org and tell us some example files (their paths) that you think Insync has deleted so that we could tell you what happened with them.