I keep having to say this - most versions of the chip have a ROM specifically for its application. Some device s- namely those on dev boards require external flash for the firmware, which can of course be changed. The external EEPROM is just for settings that the ROM uses for configuration. This allows certain parameters to be changed, but the inherent device functionality to be fixed. This works out well for manufacturers who all make essentially the same product, but with slight differences. Unless your module has >4M external flash, its a ROM chip.
As for the "beeps".. so the "beep" is coming from the host? Are these actual sounds that are played, or do they sound like glitches? The reason I ask is that, even with a totally digital stream (using a CSR64215 with S/DIF out) there is some audio sent from the host (be it phone or PC) that sounds to me like a glitch when changing certain parameters, including volume. This isn't intentional, it isn't a specific wav that is played, nor is it interference, as the entire chain is digital (save the end which is my own DAC). I haven't been able to get rid of it, although apparently disabling "low power codec" can reduce how often this occurs because it doesn't constantly turn off the output amp of the bluetooth SOC between songs or long periods of silence.
From what you describe it sounds like its coming from the PC. So this sounds isn't played when using PC speakers/wired headphones?