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Спасибо за репорт, если информация подтвердится, мы исправим эту проблему в следующей версии.

Но уже созданные теги боюсь что придется удалить вручную.

Please use English here. Sorry to hear that this problem still persists. However I haven't been able to reproduce the problem. 

We already use an ini file, it just has a "settings" extension.

What can be done:
1) Please try switching to a portable version of you use installed version, and vice versa

2) After you configure everything to your liking, store a copy of cintanotes.settings to some safe place. Later if settings get reset, you can simply copy this file to restore all your settings.

3) Try to find a way to reproduce the problem, if we have a reliable reproduction, we'll fix the issue right away.

Simply use the show window hot key and start typing

It also works in "All" mode, which is the default. Also you can use Alt+Enter and Shift+Enter to mimic Alt- and Shift- clicking on tags (NOT and AND operations)

You can enter the tag name into the search box (and even use autocomplete for that), then press Enter, and this tag will become selected on the tag sidebar.

We will start it after the release of version 4.0 with new UI. So, somewhere in 2019 is the best estimate I can make.

Thanks for the suggestion!