Supply voltage problems

In a project I’m trying to finish up, I’m powering an AVR mcu off a 3V fixed ldo voltage regulator. I want a to be able to program the mcu in circuit, but I’m not sure how to do this without damaging the regulator, since it will be powered only from the output side and the supply of the regulator will be low, making current flow back through it. If it’s allowed to do this, it will heat up a lot and fail. How do I solve this? What if I supplied the regulator normally while also powering the output supply with my programmer? I suspect it would be okay if the supply voltage of the programmer was the same as the regulator output, but I’m not sure, and I don’t want to try anything stupid.

Also, I’m having trouble preventing eeprom corruption on the mcu. If I program the eeprom with a hex file, disconnect the power supply, then reconnect it and read the eeprom, it will come out as random numbers. I believe it’s because the supply voltage takes some time to rise because there is a large capacitor on the supply side. Still, I have my BOD set at 1.8V, which should prevent this from being a problem. I’m not sure what’s going on here.

Thanks,

Mike