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nRF52 DK/PCA10040 unresponsive

Hello, I have been having issues with two different DK:s. I am doing bootloader development and suddenly the kits go unresponsive.

nrfjprog returns the following error:

nrfjprog --log -f nrf52 -r

ERROR: JLinkARM DLL reported an error. Try again. If error condition
ERROR: persists, run the same command again with argument --log, contact Nordic
ERROR: Semiconductor and provide the generated log.log file to them.

and log.log contains:

nrfjprog --log -f nrf52 -r
nrfjprog verion 9.6.0
--------------------------------------------------------------------------------
FUNCTION: open_dll.
FUNCTION: open_dll.
FUNCTION: enum_emu_snr.
FUNCTION: enum_emu_snr.
FUNCTION: enum_emu_snr.
FUNCTION: enum_emu_snr.
FUNCTION: connect_to_emu_with_snr.
FUNCTION: connect_to_emu_with_snr.
FUNCTION: connect_to_emu_without_snr.
FUNCTION: enum_emu_snr.
Out of sync , resynchronizing...
Out of sync , resynchronizing...
Out of sync , resynchronizing...
JLinkARM.dll OpenEx returned error 'Can not connect to J-Link via USB.'.
FUNCTION: close_dll.
FUNCTION: close_dll.

I have tried to replace the J-Link firmware (holding the reset button and drag-n-drop J-Link OB-SAM3U128-V2-NordicSemi 160212.bin into it). Didn't help - but it seems to have replaced the firmware because it enabled the mass storage device again (which I have previously disabled with MSDDisable).

If I try to run JLinkExe I get:

JLinkExe -if swd -device nrf52
SEGGER J-Link Commander V6.14c (Compiled Mar 31 2017 17:42:12)
DLL version V6.14c, compiled Mar 31 2017 17:42:05

Connecting to J-Link via USB...
**************************
WARNING: Out of sync , resynchronizing...
**************************


**************************
WARNING: Out of sync , resynchronizing...
**************************


**************************
WARNING: Out of sync , resynchronizing...
**************************

FAILED: Can not connect to J-Link via USB.
J-Link>

How can I get my kits working again?

Thanks.

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