1. Since the watchdog reset is a kind of Warm reset, the issue you observe looks like the effect of the ERR008587 silicon erratum, described in the i.MX6Dual/Quad Silicon Errata Rev.6.1 document:
https://www.nxp.com/docs/en/errata/IMX6DQCE.pdf
It is described for i.MX6Dual/Quad, but seems to be applicable to i.MX6DualLite as well, since the PCIe interface modules of all these processors are identical.
2. Please refer to the Section 60.6.1.1 "Reset inputs and outputs" of the i.MX6Solo/DualLite Reference Manual Rev.3 document:
https://www.nxp.com/docs/en/reference-manual/IMX6SDLRM.pdf
As it states, the WDOG reset, as opposed to POR, does not affect the ARM core Power-On Reset (that is not the same as the ARM core Soft Reset that the WDOG reset triggers on), ARM core Debug module reset, Secure JTAG Controller (SJC) reset and Secure Real-Time Counter (SRTC) reset.
Have a great day,
Artur
-----------------------------------------------------------------------------------------------------------------------
Note: If this post answers your question, please click the Correct Answer button. Thank you!
-----------------------------------------------------------------------------------------------------------------------