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I have this same issue, I migrated jobs from our old build server running 1.527 to a new server running 1.539 by copying the jobs folders over. Then I proceeded to check which of the plugins were really in use and installed a handful of those, and eventually managed to get all of the old data warnings to disappear.
Then a while later, these warnings started to appear. It doesn't seem to cause any issues, nor can I find a fix for it.