It seems a similar issue bug at 
https://bugzilla.kernel.org/show_bug.cgi?format=multiple&id=218765 

And mentions there is a related patch since v6.5 
https://www.spinics.net/lists/linux-pci/msg152506.html 

On Tue, 23 Apr 2024, Bjorn Helgaas wrote:

> FYI.  The retraining was added by a89c82249c37 ("PCI: Work around PCIe
> link training failures").
> 
> Paul, is this a regression?  a89c82249c37 appeared in v6.5.  I
> *assume* whatever is below bus 01 did actually work before v6.5, in
> spite of the fact that apparently PCI_EXP_LNKSTA_DLLLA was not set 
> when we enumerated the 00:1c.0 Root Port?

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https://bugs.launchpad.net/bugs/2085103

Title:
  pci hot plug get "retraining non-functional downstream link at
  2.5GT/s]"

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