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Cypress FS-S SPI flash devices provide a hybrid sector option where a set of eight smaller 4-KB sectors are overlaid either at the top or bottom address space. If a sector erase command is applied to a normal sector that is overlaid by 4-KB sectors, then the overlaid 4-KB sectors are not affected by the erase. Only the visible (non-overlaid) portion of the normal sector appears erased afterwards.
Such a hybrid mode is not supported by the standard Linux MTD driver for SPI flash (see drivers/mtd/devices/25p80.c and drivers/mtd/spi-nor/spi-nor.c in newer kernels). The standard Linux MTD driver only supports homogeneous flash devices with a uniform sector layout. If the hybrid sector option is not needed and has been disabled in the device configuration register, then the standard Linux driver might be used.
For applications where the small sector overlay is desired, an alternative MTD driver is available on request from Cypress. Contact technical support and provide your kernel version and ask for the corresponding FS-S Linux SPI patch.