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There are no Schengen wide regulations on how to react on visa violations and overstays. Each member state is free to set their own penalties and reactions. Overstays are usually settled with a fine, but in severe cases, you can also be banned from entering Schengen for a period of time. I can't find any current rates, but in 2011 Switzerland issued fines between 200 and 650 CHF for overstaying.
In this case, the Swiss immigration officer most probably didn't notice your overstay. When applying for a national visa, you must assume that the consulate will do a more thorough examination of your travel history, especially to the Schengen area, and that the overstay will be noticed and most likely cause problems.
You write in a comment:
It's absolutely clear that my overstaying in 28 days is fixed in data base ...
Fortunately, this is actually not the case. There is no Schengen wide database for entries and exits and even if some countries operate their own databases, the data is not complete and not suitable to track your travel history. Since currently the only trace of your overstay are the entry and exit stamps in your passport, this might actually be one of the few cases where "losing" your old passport and applying for a new one will solve your problem.