Due to a problem in the Quartus® II software version 14.0, the Rapid Recompile option may be grayed out. This option is in the Quartus II software menu Processing > Start > Start Rapid Recompile. This problem affects designs when the top level project name and revision name are different.
To work around the problem, use the following command-line option:
quartus_sh --flow recompile <project> [-c <revision>]
This problem is fixed starting with the Quartus® II software version 14.1.