Depends on how you upgraded.
You should always 'install' SDR# to new folder then copy over the plug-ins and working files. (.dll, .xml etc...)
You should never 'install' over an existing working SDR#. This would be bad.
Did you copy of the 'frequencies.xml' to the SDR# folder? (not Plugins folder)
are you using the standard frequency manager or the FreqMan plug-in frequency manager.