First of all, I think someone was having a similar problem some months ago, but that person was using a different external spellchecker (Aspell). Link.

The problem that I'm having is the following:

Flyspell wrongly considers that when a word contains accented characters, that character splits the word, thus showing spelling errors. This only happens on macOS, the same configuration on Linux doesn't produce this behavior.

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This is my setup:

I running Emacs 26.1 on macOS, installed hunspell and a dictionary in Portuguese.

Hunspell is in /usr/local/bin/hunspell, and both dictionary files (.aff and .dic) in /Users/myuser/Library/Spelling/. Running hunspell -D in the terminal lists the dictionary as available.

I configured ispell/flyspell in Emacs like this:

(when (executable-find "hunspell")
    (setq-default ispell-program-name "hunspell")
    (setq ispell-really-hunspell t))

(setq ispell-hunspell-dict-paths-alist
    '(("pt_PT" "/Users/myuser/Library/Spelling/pt_PT.aff")))

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