Ok, here goes.
Let me describe how I use LR. I have 2 catalogs. An "All Pictures" catalog and a "Processing" catalog. I use the processing catalog to import and edit pics. Save changes in xmp is checked in both catalogs. I then export original + xmp and a JPEG. I then copy those 3 files to a directory (manually) in Windows Explorer into the right folder. I then start my "All Pictures" catalog and synchronize the folder (folder is part of the catalog structure). I do this because I do not want be beholden to catalog integrity. I want to have the NEF, XMP and JEPG files and be able to synch them into any other catalog. I realize I lose the edit history doing this. I don't care. I want to be able to reproduce the final result again or make additional changes from the first import.
I recently discovered that if you do that, LR does not respect all the data that is in the XMP from the edit in the "Processing" catalog. It resets the clarity to 0 upon "Add" during the synch process. A few other things change too (Enable Profile Corrections is set to Default instead of Custom).
I lost a lot of subtle changes due to losing the clarity edits.
I found out that if I follow my old process, copy the files, then synch the folder and THEN manually re-add (over write) the altered XMP, I can then get the right settings by selecting "Read Metadata from File".
Anyone else experience this?