Kiwidude sent me the two files to look at. Here is what EPUBCheck Says:
- element "metadata" incomplete; missing required element "dc:identifier"
- unique-identifier attribute in package element must reference an existing identifier element id
So the Modify Plugin is stripping the dc:identifier which is means the OPF is now invalid. Sigil is detecting this and fixing the OPF. However, it does appear that Sigil's correction needs a bit of work since it should use the spine, manifest and any individual metadata elements when it creates the new (correct) OPF.
Where the date issue came from I don't know because I don't get that with EPUBCheck...