Huh, contrary to popular belief, I didn't need to unzip the .jar file. I only needed to do this(Using dotnetzip btw)-
//Code to delete META-INF folder
using (ZipFile zip = ZipFile.Read(jarFile))
{
List<string> files = zip.EntryFileNames.ToList<string>();
List<string> delete = new List<string>();
for (int i = 0; i < files.Count; i++)
{
if (files[i].Contains("META-INF"))
{
delete.Add(files[i]);
}
}
zip.RemoveEntries(delete);
zip.Save();
}
MessageBox.Show("Success!", "Success", MessageBoxButtons.OK, MessageBoxIcon.None);