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I have Atmega328 MCU and MAX7219 connected to each other. However, they have diode separated power sources. There is a case, when MCU will get power, but MAX7219 will not.
Would it damage MAX7219? While in the application having the knowledge that only MCU will be powered on, I will try to pull down 3 MAX input pins, but there may be some short period during MCU bootup when logical 1 may reach MAX.
Is it safe for MAX to keep it that way, considering that this situation may happen occasionally?
As you've noticed, RC on the reset pin is not going to work when you have very slow voltage rise times.
Built-in brownout detection may work, but read the microprocessor's datasheet carefully to see if there is a minimum rise time on the supply voltage.
If you are not sure built-in brownout detection will work, you can use a "voltage supervisor" chip. The basic supervisor is a three-terminal device that connects to power and ground, and pulls the output low when the power voltage is below the setpoint. Connect it to reset and you're good to go. You can buy these in a variety of voltages and turn-on delays.
Your schematic seems to have a bug. If you apply +5V from USB, then D1 is reverse-biased, and μC wouldn't get +5V.
Here's what I can propose instead. Of course, this is just a rough diagram, which shows only power distribution.
FTDI chip is bus powered only always.
When +12V source is not present, the gates of Q17 and Q18 are pulled low and the +5V rail is powered from USB.
When +12V source is present, the gates of Q17 and Q18 are pulled high and the USB section is not self-powered from the +12V supply.
MOSFET body diodes are the reason for having two MOSFETs back-to-back instead of just one. This is to prevent the USB host from getting back-powered.
Best Answer
The answer depends on why you have a diode separated power supply to begin with. You may not be achieving your original goal by tying the pins together if what you're going for isolation.
That said, in most cases a few microseconds of bad behavior on input pins of digital ICs is usually OK, in that the IC may survive it, but you may have some bad behavior when things are not within the specifications. You need to see if this bad behavior is OK for your application. It may involve, for instance, your LEDs turning on for a brief time when they aren't supposed to. If this also leads to a high current inrush through the digital inputs of your MAX, that could be a bad thing. There could be IC damage and set your uC in a reset loop if it's power supply in unable to sustain whatever the badly behaving MAX7219 demands.
This bad behavior can stay on as long and the power supplies put either device in a region where operation is not specified. The longer it keeps up, the more likely you are to cause actual damage. Its never a good idea to power things through digital lines, and that is precisely what can happen in this condition. i would recommend using a level translating buffer such as the SN74LVC1T45 and others of its family to do a better job dealing with connections across power supplies that aren't guaranteed to exist together. You simply put a resistor between the Vcc ad ground on both sides, something in the 10-100K range, and when one side loses power, the buffer shuts down and the line is effectively disconnected.