EEPROM is more general term for Electrically Erasable Programmable Read Only Memory, an evolution of the EPROM (which had to be reased w/ UV light), an (functional) evolution from PROM - one time programmable only, an (functional) evolution from ROM - content 'hardwired'/set in stone on 'build time'.
There are various types of memory cells, wirings, and control logic in use in EEPROMs which make them either a byte-wise erasable / programmable (writeable) memory, versus a Flash one which can only block-wise erasing and (mostly) byte-wise programming.
Erasing means to set all bits to 1, and programming means make some 0. Depending on cell type it can be 0 and 1 vs. 1 and 0. Depending on the 'luxuriousness' of the driver available to the application code to drive the EEPROM, the erasing and programming and byte- and block-wise operation is transparent: it is just simple read and (re)write for the application. Elaborate drivers also take care of the balanced erasing (and programming), because the prevalent EEPROMS have an 10'000...100'000 erase/write cycle limit. Technologies though get better and better and some have practically unlimited cycles and can be used like RAM (MRAM, and to a lesser extent, FRAM). Today's SSD - Solid State ('Hard') Drives fair almost unlimited.
Flash vs. 'plain' EEPROM in a nutshell: Flash is a particular EEPROM (more details).
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