Thanks again @Darryl_Menezes, that was the problem.
Here the code, if someone needs it in future (without any exception handling):
private void RunScript(bool write, string path, string newPath, ref object A)
{
string[] files = Directory.GetFiles(path);//Get all files
for (int i = 0; i < files.Length; i++)
{
Rhino.FileIO.File3dm file = Rhino.FileIO.File3dm.Read(files[i]);
string[] chunks = files[i].Split('\\');
string name = chunks[chunks.Length - 1];
string fileName = string.Format("{0}\\{1}." + "3dm", newPath, name + "_R6");
if(write)
file.Write(fileName, new Rhino.FileIO.File3dmWriteOptions() {Version = 6});
}
}