QB Issue Resolution:

If you mean that when you opened QB 2016 the first time none of your companies showed up in the No Company Open box, you need to click Open or Restore an existing company, then browse to where your QB 2015 QBW (or QBB) file is located.  Then tell QB where you want to store the upgraded 2016 company file.

Resolution for Issue 'Installed my 2016 QuickBooks Pro as a new company rather than an upgrade. Can I uninstall it and reinstall as an upgrade?' available: Yes (Solved).
Source: Intuit Community forum.

Installed my 2016 QuickBooks Pro as a new company rather than an upgrade. Can I uninstall it and reinstall as an upgrade?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Company File
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Error Recovery for Company File [Canada]
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