https://bugzilla.wikimedia.org/show_bug.cgi?id=54654

       Web browser: ---
            Bug ID: 54654
           Summary: VisualEditor: (silently) renumbering references
           Product: VisualEditor
           Version: unspecified
          Hardware: All
                OS: All
            Status: NEW
          Severity: normal
          Priority: Unprioritized
         Component: General
          Assignee: [email protected]
          Reporter: [email protected]
                CC: [email protected], [email protected]
    Classification: Unclassified
   Mobile Platform: ---

Sherry describes what happens in this edit,
https://en.wikipedia.org/w/index.php?title=Homesickness&diff=573215056&oldid=573214608
:
<<[this edit] is the original problem. It gave all of those references the same
"name" ("ref name=":4""), which convinced the software using for viewing pages
that they were all the same ref.>>

The original reporter, Christopher Thurber, describes the issue, and provides
some hints to reproduce:
<<About half of the 18 references I typed into the article on Homesickness
disappeared between yesterday and today. I was certain to follow the Save
Changes procedure, but many different references reverted to the same single
reference. [...] Same bug today. In VE, I placed the cursor in the text, chose
"Reference" from the "More" menu, added a reference, (It appeared as it should
with the appropriate numerical superscript), Saved the work, returned to check
the page...references disappeared from the list. - Window 8, Chrome >>.

TeamGale adds:
<<Hello...I have the same problem [...]. I didn't realized that it happened
while I was editing. I only saw it when I saved the article and the number of
the references had decreased. This
https://en.wikipedia.org/w/index.php?title=Michael_Giannatos&diff=next&oldid=573583391
is the change I was doing when it happened. Could it be related to editing a
table with beta? Probably not since I don't see any table on Christopher
Thurber's article. After I re-added the references and the new table, every
time I click "edit beta" the refs are gone! Before I even do any change!
Basically I can't use beta at all on this article! I don't have any issues
using the source but, if it's something simple that can be done with beta, I
prefer to do it with it. But I can't. Just wanted to say that this is happening
to other articles as well. And it's possible to happen and people don't see it.
That would be a problem to a long article with lots of references... Mozilla
21, Windows 8.>>

TeamGale again:
<<[...] every time I am trying to add a reference at a table with VE, it
changes it and replaces it with an already existent one. This time I saved the
edit just to post it here.
https://en.wikipedia.org/w/index.php?title=Dancing_with_the_Stars_%28U.S._season_17%29&diff=prev&oldid=574412488
[...] 
Update: Tables were a coincidence. It happened to me again in main article's
text. I didn't save the edit this time...>>

I think I saw this renumbering issue at it.wp as well.

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