The user configurable SFlash can be accessed either through the SWD programming interface or from CPU using firmware. A C# utility tool is provided along with PSoC Programmer to update the user configurable SFlash.
I am mentioning the path here : C:\Program Files (x86)\Cypress\Programmer\Examples\Misc\PSoC4-BLE-SFLASH-Update\Executable.
You can try to use this tool and see if it is faster.
Alternatively, please refer the below project for more details on SFLASH.