Regardless of whether it were supposedly possible to customize this shortcut in the user preferences file (*) : is there actually a default shortcut for Replace/Replace-Next ? Following shows there is no hover-help on it:

(*) After many attempts I have never been successful for the keymap.cson to be respected by Atom. It just gets ignored. Thus I want to use whatever is the default binding for Replace[/-Next] .
No, there is no default shortcut for "Replace Next", only one for "Replace All" (ctrl+enter or ⌘+enter).
But there is a built-in command for it. Putting this in my keymap.cson file works for me:
'atom-text-editor':
'alt-cmd-e': 'find-and-replace:replace-next'
I found this example from here:
https://github.com/bronson/dotfiles/blob/master/.atom/keymap.cson
All of the default settings are here:
https://github.com/atom/find-and-replace/blob/master/keymaps/find-and-replace.cson
It sounds like you already know this, but just for reference, you can find your keymap.cson file by going to Settings (ctrl+, or ⌘+,), and clicking the "Open Config Folder" button.
If your keymap.cson is being ignored, I would start to diagnose the problem by commenting out everything except those two lines in order to see if another setting in keymap.cson is broken.
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