So after all tests, migration to new tech tree was done as it was here on the first time - via marking all techs as researched despite some of them were skipped on purpose, and without triggering diplomas count in Cauldron.
But unlike here on beta, support refuse to unlearn these techs, telling that such migration is ok, and everybody should have all techs researched.
As result we can see broken accounts which show 5 diplomas in tech tree and 0-3 diplomas in cauldron, with no way for player to control that (not sure what will happen when another chapter will be fully researched, either it will show 6 diplomas or just one will be added).
@Deadeye Jerry , can you clarify Inno policy on that situation, should optional techs (those which was forcibly researched by migration) be unresearched by support on live servers on request, or affected cities (not only those who were migrated from first chapters, but higher chapters too) should suffer from disadvantage just because they are a bit older.