from what I heared this is comming up in one of the next releases of Creator. As of today, it is not possible to [program a small part of the internal flash, the current implementation is an all or nothing approach.
The programming of PSoC5 device takes place by first erasing the entire Flash and then programming the 1024 blocks.
This is a general practise as the memory memory settings has to be reset before proogramming the device (like factory upgrade, unprotected, etc).
The checksum for the flash is also calculated by taking into account the entire flash memory.