If you have multiple Revit versions installed, one of these versions will be used as default (primary) to open a RVT (or RFA) file when you double-click on it in Explorer or in other file manager.
A simple rule applies here - the RVT file will be opened in that Revit version, which was installed (or reinstalled) last, resp. that Revit, which was last launched with administrative rights (e.g. using the function "Run As Administrator").
You can set the desired version also manuály - through the Registry. Run REGEDIT and lookup the key:
In this key, edit the value (Default) to the desired Revit path (version) - e.g.:
"C:\Program Files\Autodesk\Revit Architecture 2016\Revit.exe" /dde
Do not delete the quote marks or the "/dde" parameter. Similarly, for RFA files use the key Revit.Family.