yes, when you need to alter 1 bit of an extended register that will not work.
yes the boot loader can complicate things. still think it should be possible to turn it off.
the data sheet does not mention something about turning it off. but the bit is R/W. Maybe it requires a special sequence.
or :
- first activate another clock (when it isnt)
- select a new source for the system clock
- then turn off the ext. osc.
you could ask atmel support about it.
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