when i opened it on Atom all the letters that had an accent were replaced with this symbol �
So your problem is on atom side, with a downloaded file.
I opened the same file in a notepad and I did not find this problem.
I am using UTF-8
Maybe your file is not utf-8. (Either becaue it was not utf-8 on the server or the ftp software is doing conversion for you.) By default notepad use a window encoding like window 1252 or latin-1 (iso 8859-1)
The main problem with this is that if I edit that file and upload again, this symbol(�) replaces all the accents when displaying the website in the browser.
Yes if you edit from encoding A, into encoding B and reupload it’ll still think it’s encoding A and have all character wrong.
I suggest you find native charset of your file and edit with that.
(I think it’s a longstanding problem that atom charset detection is so-so )
Alternatively maybe filezilla is doing some conversion behind the scene or your server need to be configured for utf-8