Thanks, Juan Manuel.

I normally study using PDF books. Their typography is like "hardcoded", so a post-processing using Orgmode is needed, I think.

Ypo writes:

Hi

I am copy-pasting e-books into org-mode to read and study them. 

Usually, words come hyphenated, like "ato- mized", that I wanted to
transform into "atomized". 

I am trying with query replace, but I am starting to think that it is
not the correct tool for this job. 
I tried "query-replace [a-z]-" but I don't know how to exclude the
letter before the "-".

What would you advise?

I think it will be more practical for you to use pandoc:

With this command you can convert an epub format to org:

pandoc my-epub.epub -o my.epub.org

(https://pandoc.org)

You can also install calibre and convert your epubs to plain text from
there.

Best regards,

Juan Manuel