The following code worked:
def file = new File("silent.txt")
def fileText = file.replaceAll("bop4InstallDir\\ \\=\\ myProps.cordys_install_dir\\ \\+\\ \"\\/\"\\ \\+\\ instanceName", "bop4InstallDir\\ \\=\\ \"/opt/cordys/bop4/defaultInst1\"")
file.write(fileText);