When parsing the complete XML document the contents of the <metadata> element are taken as-is. When using the API the individual members are carefully selected. Fixing this issue will require to add post-parse code that will fix the metadata element section.

Fixed upstream:

commit 7909300498fc216bbf8fcafb2b770799fb8daf2c
Author: Peter Krempa <pkrempa>
Date:   Tue Mar 3 17:50:59 2015 +0100

    conf: Remove duplicate entries in <metadata> by namespace
    
    Since the APIs support just one element per namespace and while
    modifying an element all duplicates would be removed, let's do this
    right away in the post parse callback.

v1.2.13-61-g7909300

Hi peter
Verify this bug with libvirt-1.2.16-1.el7.x86_64, still could hit the comment0's issue, can you help check it? thanks

The problem with the scenario that reproduces even with the patched libvirt is that the elements aren't actually in the described namespace but in the global one. To add the element to the namespace the following syntax needs to be used:

<foobar:herp2erp xmlns:foobar="http://foo.bar3/"/>

or similar.

Thanks peter's advise, so file a new bug 1245525 to track that issue  and verify this bug by adding the element to the namespace, the verify steps as following

pkginfo
libvirt-1.2.17-2.el7.x86_64

steps
1.Prepare a shutoff guest
# virsh list --all
 Id    Name                           State
----------------------------------------------------
 -     7.0                          shut off

2.Edit guest's xml, add multi same metadata in guest's xml, save the guest's xml, only 1 record will generated
#virsh edit 7.0
--
  <metadata>
<foobar:herp2erp xmlns:foobar="http://foo.bar3/"/>
<foobar:herp2erp xmlns:foobar="http://foo.bar3/"/>
<foobar:herp2erp xmlns:foobar="http://foo.bar3/"/>
<foobar:herp2erp xmlns:foobar="http://foo.bar3/"/>
<foobar:herp2erp xmlns:foobar="http://foo.bar3/"/>
<foobar:herp2erp xmlns:foobar="http://foo.bar3/"/>
<foobar:herp2erp xmlns:foobar="http://foo.bar3/"/>
  </metadata>

#virsh dumpxml 7.0
  <metadata>
    <foobar:herp2erp xmlns:foobar="http://foo.bar3/"/>
  </metadata>


3.Do some basic check the metadata command, all command could get expect result.
# virsh metadata virt-tests-vm1 --uri http://foo.bar3/
<herp2erp/>

# virsh metadata virt-tests-vm1 --uri http://foo.bar3/ --edit --key foobar
<herp2erp1/>

# virsh metadata virt-tests-vm1 --uri http://foo.bar3/ 
<herp2erp1/>

# virsh metadata virt-tests-vm1 --uri http://foo.bar3/  --remove
Metadata removed

# virsh metadata virt-tests-vm1 --uri http://foo.bar3/ 
error: metadata not found: Requested metadata element is not present

According to upper steps, mark this bug veried

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory, and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

https://rhn.redhat.com/errata/RHBA-2015-2202.html