Joe (and Kevyn), my last comments on this issue...
The camcorder that Kevyn mentioned (thanks for the info, Kevyn) uses a media structure with (likely) DCIM, MISC, and PRIVATE folders/directories on the SD card (FAT32, ExFAT, etc.). The PRIVATE folder would (likely) contain an AVCHD folder, with BDMV and STREAM folders inside (amongst others). I would imagine that the actual video files are .MTS files.
So, it seems like the SD card was processed and the video was re-wrapped or transcoded to get the .mov files. How the transfer was done is of interest.
It would be useful to see if there is any difference in the metadata of one of the problem files and one of the files from the same source that has the .mov extension.
I believe that once imported into FCP, video files may also be referenced (internally, by the SQLite DB) by their inodes rather than the just filename, which could expain why removing a filename extension wouldn't affect the file's use in the current FCP Library after import (and not yield a "missing media" warning). However, on export to XML, the actual filename must be used in the filename URL schema.
[Side note: I wonder if how media is referenced in FCP's DB is why drive formats other than HFS+ and APFS are not recommended/supported.]
Are the missing filename extensions a result of filename changes after the media was imported and used initially, or was it something that happened when media was copied from drive to drive? Were the problem files imported at a different time than the good ones (with .mov extensions)? Was the method of import into FCP different (via direct import of the video files, or using the SD card structure, or from a camera card archive)? This issue seems to be more of a "DIT" or assistant editor media management issue than anything to do with FCP specifically.