Syncing keymaps between Linux and Windows not working

I have set up the settings repo in the github so to have both IDE settings syncing correctly. After some customizings in the shortcuts in Windows (added hotkeys for the bookmarks, surround etc.).As a result I get the Windows copy keymap. I overwrite remote repo settings using the menu "File-Manage IDE Settings-Sync with Settings Repository-Overwrite Remote". On my Linux machine I import the same settings using the command "File-Manage IDE Settings-Sync with Settings Repository-Overwrite Local". Everything works perfect. I can see the Webstorm creates in my remote repo the folder named "Keymaps" with a Windows copy keymap within. But after some time this folder gets gone from the remote repo (no "Keymaps" folder) and my custorm Windows copy keymap vanishes as well. I noticed it happened 3-4 times. I tried to use the merge opt in place of overwriting but no success. I got too exausted to configure my shortcuts every time from the scratch. How could I syncronise correctly my Windows and Linux machines?