Notice the two different local records
Suppose a movie folder contains movie.nfo and Harbour Film.nfo beside Harbour Film.mkv. Those filenames are an invented example. Kodi’s movie NFO guide recommends matching the video filename. It also documents a special movie.nfo case tied to the setting that says movies occupy separate title-matching folders. The presence of both files is therefore a configuration question, not proof that either file is corrupt.
An export can create the second file
Kodi explains that a Separate Files export writes the filename-matched NFO even if movie.nfo was used before. With the relevant folder setting still enabled, a later refresh can prefer movie.nfo. Changes exported to the other file may consequently appear to have been ignored. Preserve both records while checking their contents and the source configuration; deleting one without comparison can discard information you intended to keep.
Settle the naming convention before repeating the import
Choose a documented naming arrangement for the collection and test it on one item. Compare the synopsis, watched information or other field you deliberately changed, then use the appropriate refresh operation. A successful library export is not a backup of the original full-quality artwork: Kodi’s export overview says cached images are optimised versions. Keep original media and artwork separately, and record the naming choice so a later export does not silently restore the same conflict.
Questions, answered
Does the newer modification time automatically make one NFO authoritative?
The documented naming and source-setting rules determine which file Kodi reads; do not assume newest wins.