Are you sure you're not
overwriting something with those additions? I'm only asking because I can add those three items to existing epubs and save them with no broken/rebuilt OPFs.
My guess is you might be overwriting the
existing dc:indentifier entry—which is also being referenced as the unique-identifier in the "package" tag. That
will result in a broken/rebuilt OPF. You'll want to
add the ISBN identifier to the dc-metadata... not overwrite the existing one.
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Edit: And when content.opf file is rebuilt, all the files in the spine lose their order. Why is that?
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In short... the spine order is lost BECAUSE the opf had to be rebuilt. It also loses the metadata that was previously defined. I realize that's not a very satisfying answer, but it's why I always make sure I have a good backup copy of the epub before I make any manual changes to the OPF... because one simple "Save" when your OPF file happens to be in a funky state, and you suddenly have a lot of stuff to fix.
One more reason to use Sigil's GUI metadata editor to initially add new metadata. You can always alter the details manually later if need be.