The normal "start debug" function will always program the device and this will erase the memory.
But there is also a "debug without Programming" option. This of course will only work if you didn't change your firmware.
You can also add "debug without programming" to your program tray:
I assume there might be also a linker or project setting to prevent this, but I am not sure about that at the moment.
That worked for saving the data between debug sessions.
Is there a way to define the areas the programmer touches so it leaves the EEPROM area alone?
You can prevent the EEPROM area from getting programmed by following the steps below:
1. In PSoC Programmer, click on the Load from device option.
2. Uncheck the WFLASH[32K] memory area.
In doing so the PSoC Programmer skips programming of the EEPROM area and you can retain your previous data.