I have a collection of photos that I'm organizing by the metadata field SubSecDateTimeOriginal. I edited some IPTC metadata field (creator, city, etc.) and also changed the rotation of a few images. Using Exiftool I got the metadata for the files before and after these edits. The "after" files have SubSecDateTimeOriginal scrubbed at random, which doesn't seem like it should happen. I didn't edit the date, so this field should remain unchanged.
I wasn't able to reproduce that with a JPEG containing EXIF:SubSecTimeOriginal. Are you able to provide a recipe (and perhaps sample files) for reliably reproducing the problem? Unfortunately, without a way to reproduce the problem, Adobe is very unlikely to look at the issue.