diff --git a/doc/bugs/android_sync_messes_tree/comment_3_f964c18aced83ba02d3436941dbcbacc._comment b/doc/bugs/android_sync_messes_tree/comment_3_f964c18aced83ba02d3436941dbcbacc._comment
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+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 3"""
+ date="2022-10-04T17:13:21Z"
+ content="""
+Here's my suspicion: You started with annex-tracking-branch set to
+some value, and synced. Then you changed it to some other value and synced
+again.
+
+For example, if you start with it set to master:subdirectory, then
+change it to master, this happens on the subsequent sync:
+
+	list directory ok
+	update refs/remotes/directory/master ok
+	
+	Updating d946446..8dd4a6f
+	Fast-forward
+	 bigfile                           | 1 +
+	 foo                               | 1 -
+	 subdirectory/bigfile              | 1 -
+
+So, files not in subdirectory get removed, and everything in subdirectory
+is moved out of it and into the top of the tree.
+
+Does this behavior make sense? I am not sure, but by changing 
+annex-tracking-branch, you have certianlly ripped the rug out from under
+git-annex. And that seems to more or less match what you are describing.
+
+(Nothing to do with being interrupted, and no merge conflicts though.)
+"""]]
diff --git a/doc/bugs/android_sync_messes_tree/comment_4_1f819796ec13f83e56917332efffe54d._comment b/doc/bugs/android_sync_messes_tree/comment_4_1f819796ec13f83e56917332efffe54d._comment
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+++ b/doc/bugs/android_sync_messes_tree/comment_4_1f819796ec13f83e56917332efffe54d._comment
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+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 4"""
+ date="2022-10-04T17:21:44Z"
+ content="""
+The reason that happens is that the remote tracking branch has a tree with
+"subdirectory/bigfile" and "foo" in it. The new tree imported from the
+remote, after changing annex-tracking-branch, has "bigfile" in it. So the
+result is the same as if a regular git remote used to contain that old
+tree, and has been updated to the new tree. `git merge` with a remote where
+that has happened naturally updates master to move "subdirectory/bigfile"
+to "bigfile" and to delete "foo".
+
+I think this does beg the question of how to safely change
+annex-tracking-branch. One way is to sync, change it, sync again. Then
+revert the commit that imports from the remote. That gets the tree back
+into the state it was before, and then syncing again will update the
+remote.
+
+Perhaps git-annex should detect when the annex-tracking-branch config
+has changed, and somehow handle this better, or just refuse to sync?
+"""]]