Not sure what was the main problem, but "Copy settings wizard 2016" was doing absolutely nothing (win 8.1, SW2016 Sp3) - not copying any settings. I was trying to restore settings which were backed up via "Copy settings wizard 2015" with SP5. After playing a little bit I noticed, that on newly created Windows user, this Copy wizard works - with condition that the wizard is executed BEFORE the first launch of Solidworks in that newly created user account.

So I found the solution: you have to delete all user specific files and registry keys in your current account, and then execute wizard BEFORE launching the solidworks. In order to clean up current user, I followed instructions from Javelin tech manual (attached), and deleted everything (files and registry keys) which are referred to current user (nothing outside it - nor program files folder or anything else).

After deleting everything and restoring the settings -Solidworks launched just like for the first time - warning for changed menus, license agreement etc. Setting were copied.

HINT: do not miss the SRAC folder in registry - it won't work if you leave it

Hope this could be useful for somebody