I'd tried turning off save_on_focus_lost right after this strange behavior revealed itself the first time but with no effect. Files tend to be saved when view gains focus, not on focus lost.
Combining it with hot_exit=false does not help too.
Never mind, being highly annoying at first day of usage this drawback became almost unobtrusive in a week. I'm already used to click any other sidebar item or tab right after deletion to eliminate it =)
Probably the best way to solve the problem (deleted files get re-created) is to make sublime close the view on the file when pressing delete. I am sure it can be achieved by setting up a macro with close and delete but having this as default behaviour of delete would be cleaner.
I ran into the very same problem. Turns out autosave feature has nothing to do with the problem, this is Git plugin who is responsible. To solve put following config to User/Git.sublime-settings:
For me the culprit was the Modific package (similar to what Alexander posted), this user setting solved it:
Holy shit, I have installed modific too. And I'd never suspect it of such sabotage. Thanks, Daniel.
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