Thanks for the report - I don't think this issue has come up before for the WM.
Which version USR did you export from the Waypoint Manager, and do you know which version you exported from your HDS?
Did you delete waypoints on the HDS before reimporting your updated file? (I don't know if this would effect things, but might be useful info for me).
Are you willing to share your original and updated USR files so that I can take a look? Discretion assured, of course, you can mail to This email address is being protected from spambots. You need JavaScript enabled to view it.
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Whilst we try to understand what is going on with this file, you might be able to get your waypoints back into your HDS by exporting from the WM in either GPX or a different USR version. I would suggest anything USR 4 or later.