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General question about EEPROM

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Hi
I recently had a problem with my dev kit- when I plugged it in to my computer, it showed up as a USB serial device as opposed to a USB blaster. The extremely helpful forummers here informed me that my EEPROM was corrupted, and the FT Prog tool supported this- after running the scan and parse, the device showed up as all 1s (FFFF).
On the other hand, when I got the board and plugged it in, there seems to be a program left from the previous user- one of the switches turns on a LED. I assume that this program is loaded to the FPGA from the EEPROM
So how can this be both ways- the EEPROM is corrupted that it does not support USB blaster, but it loads a program onto the FPGA?
Thanks

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