Sync is not working correctly from .jpg to .nef

I am working on editing a large collection of photos, maybe 150 or 160. These are photographs of flat art taken using a flat-art photography stand (camera points directly at floor, art piece is on larger white background). I have two versions of the exact same image, one .jpeg and one .nef. I am editing them one at a time, fixing the white balance, any accidental tilt, and cropping them. Again, the two images are exactly the same: size, angle, etc. What I have been doing is editing the .jpg and then highlighting the .nef version and syncing the two. This has been working perfectly, but something has changed and I don't know what I did to cause it. When I sync the changes I have made to the .jpg, the crop does not line up correctly on the .nef image. Instead of the image being perfectly centered and cropped, it is off to the side, revealing the white background and cutting off the image. Why is this happening? How can I fix it?

What dj wrote regarding crops is equally true for all and any edits you do to the NEF, including any you paste from the jpg. Those edits exist only in the catalog  and additionally in an XMP file if you opt for that. Thus the modifications to the NEF will be viewable only in your LR catalog or by somebody else (with the accompanying XMP) in Adobe software.
Also, you should consider that color-critical edits cannot simply be pasted from a gamma corrected image rendered in a narrow  RGB space to linear and wide gamut image data and be the same.  If it's a jpg from the camera it is in either sRGB or Adobe RGB, narrower gamuts than LR's linear ProPhoto RGB and colors have already been changed in the camera by both the Rendering Intent and the Tonal Response Curve. Moreover, the camera's jpg has been built on a Nikon camera profile while both viewing within LR and exports from it are on the basis of an Adobe profile that may seek to emulate the maker's profile but will never be the same.
You say you do WB adjustments to the jpg. How are +/- tweaks in a limited range applied on top of the camera's WB supposed to translate to WB for the NEF when even the UI (Temperature and Tint) is different?
I have had many years experience photographing paintings for show catalogs and your method seems fundamentally flawed to me.

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