I don't know about Kindle, but I wait till after Calibre closes the 'on device' column, before I reach for the cord.
If you manage to
only corrupt metadata.calabre.
Shut-down Calibre
completely, then delete the corrupt file.
Then start Calibre and WAIT while it re-scans your K3 (can take a bit of time. Go play with the cat

while you wait.)