Could you help check the JTAG connection as well?
Some device are failed to connected by JTAG. Thanks.
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To clarify is the issue the devices cannot connect, or that the devices loose connection?
Pin 5(PD) should be connected to the VDDIO supply of the MCU, as this pin is used by the Emulator pod to confirm there is power good to the device. If this 5V is from upstream supply that also goes into whatever LDO makes the 3.3V for the MCU this should be OK since power in one domain should mean power in the other.
We have no recommendation for the PU resistors on TCK/TDI/TMS, while this may be a best practice to not leave an input pin floating, I would make sure whatever emulator pod is being used can overdrive these PUs. Likely this is OK, but you could try and remove these and see if the issue goes away.
I beleive that the EMU0/EMU1 resistors are too weak, we recommend 2.2k-4.7kOhm in the DS. It is important that when TRSTn goes inactive these both are high else the device may latch into boundary scan mode(EMU0 =high and EMU1 = low) I'd also put a scope probe on EMU0/1 and TRSTn to confirm the pin states are OK.
Finally, we also need to consider the layout of the signals. How much distance is between the JTAG header and the MCU? Is there one or two traces that have a much different trace length than the others(especially for TCK/TDI/TMS/TDO).