Well, what I explained above, applies to "Stamp Visible", not to "Merge Visible".
I think what you are doing is this:
You open an image, edit using adjustment layers, then copy the BG layer. (Cmd+J is faster then drag to the "copy layer" icon
)
You then run the High Pass filter on the "Background copy" layer, and set blend mode Overlay or one of the other Contrast blend modes.
Then you do "merge visible", and your image changes?
I have tried, but *cannot* duplicate this.
If I take this image (sorry for the garish colors; not colormanaged screenshot), and use "Merge Visible" now, the image stays identical...
I know I've seen it happen before however, and I think it had something to do with blend modes or clipping masks or so. Cannot remember what it was, and cannot replicate it either.
I'm curious what's happening though.
Can you post a screenshot of your layers palette, or put the .psd online somewhere to download? (small version like 600 px wide is plenty, as long as it's layered)