Can someone give me more information about how to reproduce this issue?
I tried to change the file system order of the sphinx documents, but got
identical results:

$ tar xjf testcase.tgz
$ cd testcase
$ make html
$ cp build/html/objects.inv .
$ ls -U source/
_templates/  _static/  conf.py  index.rst  file1.rst  file2.rst
$ cp source/file1.rst foo
$ rm source/file1.rst 
$ mv foo source/file1.rst
$ ls -U source/
_templates/  _static/  conf.py  index.rst  file2.rst  file1.rst
$ rm -r build && make html
$ cmp objects.inv  build/html/objects.inv


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