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I can confirm this on Atom v0.151.0-85fae83 on Mac OS X 10.10.1, though it isn't caused specifically by saving ... but by the act of tabifying or untabifying. You can prevent it from wiping out your bookmarks on every save by setting the onSave value to none.
I'm looking into what is actually causing this to happen.
So it appears that this is caused by a TextBuffer.scan with replacements followed by a save operation. I replicated it just using the JavaScript console in Atom:
I'm going to file a bug on Atom Core and link it here.
It actually doesn't have anything to do with the save operation, but it has to do with some sort of interaction with the decorations API that bookmarks uses and the TextBuffer.scan method when used to replace whitespace.
It looks like tabs-to-spaces is clearing all bookmarks when I save any file.
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