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OTA DFU hardware resources

I have a strange problem trying to use timer1 in a trivial app that's loaded via DFU. I can't get delays longer than about 1 second, despite having the prescaler set to 9. So I am wondering if the DFU initialization has changed some register associated with timer1.

Also, I would like to modify the DFU code such that the LED flashes, instead of being on solidly, and I wondered if I can use a timer and PPI channel to do this without screwing the bootloader.

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