What version of PT3 are you using? (see the title bar of PT3)
If it's not Beta 30.8 please update.
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PT3 Build History / Release Notes
To clear the duplicates do File > Setup Wizard; this will import and move all of your existing hand history files.
Then make sure that the 'move processed files to' option is enabled.
Tutorial: Using Auto Import
If you still get the import errors please
report your problem so that we can investigate.