You might be able to solve this if you have a text editor with good encoding support. That way, you could switch between the Latin 1 and the UTF-8 encoding until you have the right combination. I use SubEthaEdit which can convert but also reinterpret a file when you change the encoding.
The ç should be encoded as c3 a7 in UTF-8 when you view them as bytes. What could be happening here is that the file was interpreted as Latin 1 first, where c3 a7 means ç, and then saved as UTF-8, where ç is saved as c3 83 c2 a7. You want the c3 a7 version.
The way to get back to a nice ç is to open the file as UTF-8, save it as Latin-1, and then open it again as if it was UTF-8.
Once you did this, you can import the file into MySQL, but specify it is UTF-8, otherwise MySQL might try to interpret it as Latin 1 and you will still have the ç characters.