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There are likely to be two separate issues here:
The first is that you need to reset the file association at the OS system level for PDF files to be whatever reader you want. It sounds as if you have set it to be the Calibre viewer. You do not mention your OS so it is not easy to try and give more detailed steps.
The second issue is for viewing PDF files from within Calibre itself. You can select whether to use the Calibre viewer or the system viewer (recommended) for each file type under the Calibre Preferences->Look and Feel->Behavior option.
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