the most important thing is, that the problem is solved and you can go ahead with the website.
About editing the files: you can use whatever editor you prefer. The only requirement for the editor: it has to give the option to store the files as UTF-8 without BOM. I guess all but the simplest editors allow to do so (famous exception: Windows Notepad), perhaps even the editor of your FTP client (you can have a look at its options). Or perhaps you can choose another editor as editor for your FTP client (as is described for FileZilla/Notepad++ here: http://linhost.info/2008/01/notepad-and-filezilla-tip/).
I for myself like editing files online on my server too, instead of download, edit, upload. Fortunately I can do this with my familiar editor (Komodo Edit -- probably a bit heavyweight for occasional editing) by "Open Remote File". A nice alternative too.