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I use dates in org-mode(C-c .) and the format is like this:

(setq-default org-display-custom-times t)
(setq org-time-stamp-custom-formats '("<%Y-%m-%d>" . "<%Y-%m-%d %a %W %H:%M>"))

It parses the date in the format:

<2020-08-20>

On the other hand I open the org-mode files with different text editors and under the hood the format is:

<2020-08-20 чт>

Is this how it normally works? Is there any way to change the date format of org-mode's date C-c . to print without the day, just as seen as in the org file?

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That's how it normally works: Org mode has to have a given date format so that it can parse dates with the date parser that is built in to it, so you don't get any freedom on how the dates are stored in the file. OTOH, emacs allows overlays so dates can appear in a different format when you display the buffer. But that is purely for display and is not reflected in the storage format.

There are ways to actually force the displayed format to be written to a file, but it may well happen that Org mode will not be able to parse the resulting file properly. See e.g. https://github.com/mneilly/Emacs-Persistent-Overlays for one such attempt. ISTR another such attempt mentioned here in Emacs SE, but I cannot find it ATM.

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