Multi app bootloader has different applications. It genarerates two cyacd files for each bootloadable application (which ends with _0 and _1). The bootloader host looks at the the filename end to understand the application number. Later, it sends command to the bootloader to understand the active application in device.
In the case of a normal bootloader , the active app comand is not a recognised and this error is generated.
Please rename the bootloadable project so that it does not end in _# such as SC6_1 in your case.
Thank you very much geon. That fixed the problem.