metadata.opf is indeed a calibre generated replica of the books metadata (as seen).
And yes, it runs slowly in background (to avoid performance hits) on every change. You can check how many are yet to be posed/updated
right-click the Library Icon: Library Maintenance: Library Metadata Backup Status
SFC checks the Windows install,
Disk maintenance tools (chkdisk) will check the file system
You might recover some books from your device