nRF52840 DK permanent hang during flashing


We have a stability issue with nRF52840 DK after it has been upgraded to JLink DLL version V6.60e and firmware OB-SAM3U128-V2-NordicSemi compiled Jan 7 2019 14:07:15.
Please see the below scenario which typically reproduces this problem:

1) Start JLinkExe

16:36 $ sudo JLinkExe -if swd -speed 9600 -device NRF52840_XXAA -autoconnect 1
SEGGER J-Link Commander V6.60e (Compiled Jan 17 2020 17:28:37)
DLL version V6.60e, compiled Jan 17 2020 17:28:19

Connecting to J-Link via USB...O.K.
Firmware: J-Link OB-SAM3U128-V2-NordicSemi compiled Jan 7 2019 14:07:15
Hardware version: V1.00
S/N: 683122431
License(s): RDI, FlashBP, FlashDL, JFlash, GDB
Device "NRF52840_XXAA" selected.

Connecting to target via SWD
InitTarget() start
InitTarget() end
Found SW-DP with ID 0x2BA01477
Scanning AP map to find all available APs
AP[2]: Stopped AP scan as end of AP map has been reached
AP[0]: AHB-AP (IDR: 0x24770011)
AP[1]: JTAG-AP (IDR: 0x02880000)
Iterating through AP map to find AHB-AP to use
AP[0]: Core found
AP[0]: AHB-AP ROM base: 0xE00FF000
CPUID register: 0x410FC241. Implementer code: 0x41 (ARM)
Found Cortex-M4 r0p1, Little endian.
FPUnit: 6 code (BP) slots and 2 literal slots
CoreSight components:
ROMTbl[0] @ E00FF000
ROMTbl[0][0]: E000E000, CID: B105E00D, PID: 000BB00C SCS-M7
ROMTbl[0][1]: E0001000, CID: B105E00D, PID: 003BB002 DWT
ROMTbl[0][2]: E0002000, CID: B105E00D, PID: 002BB003 FPB
ROMTbl[0][3]: E0000000, CID: B105E00D, PID: 003BB001 ITM
ROMTbl[0][4]: E0040000, CID: B105900D, PID: 000BB9A1 TPIU
ROMTbl[0][5]: E0041000, CID: B105900D, PID: 000BB925 ETM
Cortex-M4 identified.
Reset delay: 0 ms
Reset type NORMAL: Resets core & peripherals via SYSRESETREQ & VECTRESET bit.
Reset: Halt core after reset via DEMCR.VC_CORERESET.
Reset: Reset device via AIRCR.SYSRESETREQ.
****** Error: Communication timed out: Requested 12 bytes, received 0 bytes !

2) Start JLinkRTTClient to see logs from device

3) Start flash programming

sudo nrfjprog -f nrf52 -r --program nrf52840_xxaa.hex --sectorerase
ERROR: nrfjprog failed for an unknown reason. Run the same command again with
ERROR: argument --log, contact Nordic Semiconductor and provide the generated
ERROR: log.log file to them.

In step 3) the programming does not start and below error appears in JLinkExe:
****** Error: Communication timed out: Requested 12 bytes, received 0 bytes !

nrfjprog -i does not show any connected SWD device when this problem appears.

Rebooting PC with Linux with nRF52840 DK in such state causes that PC hangs on bootup. It's very problematic for us, since we are working remotely with this setup.
The only way to recover the nRF52840 DK is to physically disconnect it from USB and then reconnect.

Please let me know if there is some solution to this issue, because it's very problematic in our development.