For a start, you never put back all the \n characters that you've removed.
fprintf(fid, strjoin(A, '\n'));
may work. However, you're playing with fire here as you're interpreting binary data as text. There's no guarantee that the binary data will survive the round trip unaltered (e.g. the binary data forms an invalid character that could be ignored by regex).
And of course, it's possible that he binary data includes offset indicating where to find other binary data into the file, if you change the length of the header the offsets will point to the wrong location.
It's very unusual to have a file that's text and binary. It may be that some of the binary content is some textual data, but it should still be interpreted as binary. Usually text in a binary file is either fixed length, prefixed by binary data indicating how long the text is, or \0 terminated.