The Convert Programming Files utility within the Quartus® II software has an option, Advanced > Disable AS mode CONF_DONE check which can be useful for debugging AS mode configuration problems.
This option can be enabled when creating an AS mode configuration file using the quartus_cpf command line utility by including the --ignore_condone_check=on
option.
For more details on this option and other options available within the quartus_cpf utility, type:quartus_cpf --help=option