I don't think updating from Update Site will update the eclipse.ini file: you need to fix it.
-startup
plugins/org.eclipse.equinox.launcher_1.4.0.v20161219-1356.jar
--launcher.library plugins/org.eclipse.equinox.launcher.win32.win32.x86_64_1.1.500.v20170531-1133
However, if you simply want to keep your preferences and your plugin, I suggest you to use Eclipse for that:
In Oxygen.1 (or the updated Eclipse), you can install feature/plugins
- using an existing installation (go to File > Import then select *Install > From Existing Installation)
- using an exported software item (go to File > Import then select *Install > Install Software Items from File)
For the second option, you need to export it first on the previous Eclipse using File > Export > Install > Installed Software Items to File.
Note: the Eclipse directory store little configuration (at least, it store the known workspaces/update site). This link here might be of interest.