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The main problem with that is that when you feed 5V into the inputs, the protection diodes will clamp it to your 3.3V rail, and because you use series pass regulation then your 3.3V will rise to about 4.3V and most likely kill the rest of the components on the 3.3V rail.If even HVP doesn't work then it sounds like you burnt the chip. I found a good way to kill AVRs was to power it from 3.3V and then feed it 5V signals. In the data sheet they quietly mention that the voltage on any pin has to be within 0.6V of Vcc. Otherwise I've found them to be pretty resilient in my experience.
The main problem with that is that when you feed 5V into the inputs, the protection diodes will clamp it to your 3.3V rail, and because you use series pass regulation then your 3.3V will rise to about 4.3V and most likely kill the rest of the components on the 3.3V rail.
Yes they have them, any CMOS-process chip has them in order to prevent SCR latchup.
But if you have light load on the 3.3V rail and the voltage source attached to the input can supply more current than the load needs, then it will rise the rail to whatever it wants and destroy anything that doesn´t like such overvoltage.
See here for reference: http://www.atmel.com/images/atmel-8159-8-bit-avr-microcontroller-atmega8a_datasheet.pdf page 49