Saving Metadata (cmd +S) into the file changed the Capture Date / Time

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These symptoms occur with photos missing the metadata field EXIF:DateTimeOriginal (the industry standard field for recording capture date).  For such photos, LR uses the file's last-modified time for its notion of capture date. But when the last-modified time changes, such as when you do Metadata > Save Metadata To File, LR immediately updates its notion of capture date with the new last-modified time.

Adobe considers this behavior "as designed". There are other bugs in LR's handling of photos missing EXIF:DateTimeOriginal, but this is the strangest.

You can tell if a photo is missing EXIF:DateTimeOriginal by looking at the Metadata panel's EXIF tagset:

The workaround is straightforward: Select the affected photos, do Metadata > Edit Capture Time, and immediately click Change All.  This does not, repeat not, REPEAT NOT, change all the photos to the same date. Rather, it sets each photo's EXIF:DateTimeOriginal field to have the capture date that's currently displayed in the Metadata > Default > Capture Date/Time field.   It's harmless to do this on photos that already have a value in EXIF:DateTimeOriginal.

For the photos whose last-modified times have been changed by Metadata > Save Metadata To File, you'll have to either recover previous versions from backup, change them manually using Metadata > Edit Capture Time, or use the Exiftool utility to see which file and metadata dates might still be useable, if any.

All Captured using a digital camera... The files were converted to DNG on import / JPG were left as JPG Files. It's a clients catalogue so I can’t be specific about the camera model.

But as I indicated the initial import process was to import into a Subfolder / Organized by Date

Cmd+S normally does not change the capture date of a file captured on a digital camera, although I've seen happen with scanned files. Therefore, it would be helpful if you provided details on format and source of the problem files. Are they Raw, JPEG, TIFF, PSD, and were they scanned or oginally captured on a digital camera?