### Please describe the problem.

Syncing two repositories causes many files that are on both systems to be deleted.

My computers A and B have a directory with 1600 files taking 500MB.   I'm trying to sync A to B thus:

git annex sync --no-commit --no-push

This immediately deletes those 1600 files from B.   (Before I added -no-push it also deleted those files from A).

Recovering from this with git reset --hard takes 13 minutes, so it's difficult to run experiments.   However I have spent about a full day on this over the last week.

### What steps will reproduce the problem?

This repository has evolved over time so I can't give a MWE.   However, I created the git repository before initing annex, and did some more work before adding the largefiles option.   It's probable that something inside annex is now badly confused.

I don't expect you to solve my particular problem from this report.   However, sync has a major hidden problem. 

### What version of git-annex are you using? On what operating system?

20160511-1.
the annex is v6.
the OS is Ubuntu linux  4.4.0-38-generic 

### Please provide any additional information below.

[[!format sh """
# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log


# End of transcript or log.
"""]]

.git/annex has no log files, even in subdirs.

There have been occasional reports going back years from other people reporting that sync destroyed massive amounts of their repositories.    That this bug persists suggests that the problem is subtle.

I upgraded my annexes to v6 because the concept of locked and unlocked looks good.   Then, when researching my problem before posting this bug report, I found a comment that upgrading to v6 is not (now?) recommended because of possible bugs.   It would have been nice if this warning were more prominent.

### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)

The idea is great.  Preliminary tests were quite positive.   That's why I tried it on my big repositories.


> git-annex sync does not do anything to a working tree that git commit 
> and git pull doesn't do. I sync repos all the time and have never seen
> anything like this. Without a way to reproduce such a bug, I have to
> assume it was some kind of user error. [[done]] --[[Joey]]
