Cycling power on ATmega32U6 during a debug session may cause a loss of sync with the device
Single stepping GCC-generated code in source-level may not always be possible. Set optimization level to lowest for best results, and use the dis-assembly view when necessary.
Setting the target clocks (debugging and programming clocks for JTAG) too low, typically below 100kHz or running a debugWIRE target at slow frequencies might result in errors in Atmel Studio due to timeouts being to short to handle the time it takes to complete some commands in the Atmel AVR ONE! emulator when using these low frequencies. This problem increases as the target device memories increase in size and as the number of active software breakpoints increases.