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Sometimes the HDR merge feature works just fine. Sometimes it shows a different image in the preview windor. Have restarted many many times.
Showing us a screen shot or shots of what you are seeing will help to solve the problem you are having.
One thing to try, extra work, but useful as to keep what you are merging away from all the clutter.
In LrC, using the Folders Panel, create a new folder, name it Merge in progress,.
Move the photos for one photo merge into this folder.
If anything is stacked (a possible issue) then unstack (unstack just in case the stack included a wrong photo)
With just that one set attemt the merge
When done you can move the images back or to any folder you like.
Point is to isolate the bracket and look for anything off.