Hi Tim,
Our test engineer use ubuntu 24.04 reproduce this issue. They do hot repmove 
and hot plug on nvme device. And you can see, the nvme 7 downgrade to 2.5GT/s 
while nvme 6 is normal pcie link, they are the same type of nvme device.
kern  :info  : [  288.320053] pcieport 0000:86:02.0: pciehp: Slot(30): Card 
present
kern  :info  : [  289.115131] pci 0000:87:00.0: [1344:51c3] type 00 class 
0x010802 PCIe Endpoint
kern  :info  : [  289.115176] pci 0000:87:00.0: BAR 0 [mem 
0x00000000-0x0003ffff 64bit]
kern  :info  : [  289.115226] pci 0000:87:00.0: ROM [mem 0x00000000-0x0003ffff 
pref]
kern  :info  : [  289.115241] pci 0000:87:00.0: Max Payload Size set to 512 
(was 128, max 512)
kern  :info  : [  289.115375] pci 0000:87:00.0: PME# supported from D0 D1 D3hot
kern  :info  : [  289.115816] pci 0000:87:00.0: Adding to iommu group 40
kern  :info  : [  289.118666] pcieport 0000:86:02.0: ASPM: current common clock 
configuration is inconsistent, reconfiguring
kern  :info  : [  289.124069] pcieport 0000:86:02.0: bridge window [io  
0x1000-0x0fff] to [bus 87] add_size 1000
kern  :info  : [  289.124085] pcieport 0000:86:02.0: bridge window [io  size 
0x1000]: can't assign; no space
kern  :info  : [  289.124089] pcieport 0000:86:02.0: bridge window [io  size 
0x1000]: failed to assign
kern  :info  : [  289.124092] pcieport 0000:86:02.0: bridge window [io  size 
0x1000]: can't assign; no space
kern  :info  : [  289.124095] pcieport 0000:86:02.0: bridge window [io  size 
0x1000]: failed to assign
kern  :info  : [  289.124099] pci 0000:87:00.0: BAR 0 [mem 
0xd4600000-0xd463ffff 64bit]: assigned
kern  :info  : [  289.124112] pci 0000:87:00.0: ROM [mem 0xd4640000-0xd467ffff 
pref]: assigned
kern  :info  : [  289.124115] pcieport 0000:86:02.0: PCI bridge to [bus 87]
kern  :info  : [  289.124121] pcieport 0000:86:02.0:   bridge window [mem 
0xd4600000-0xd46fffff]
kern  :info  : [  289.124125] pcieport 0000:86:02.0:   bridge window [mem 
0x1e6000000000-0x1e60001fffff 64bit pref]
kern  :info  : [  289.124694] nvme nvme6: pci function 0000:87:00.0
kern  :info  : [  289.124713] nvme 0000:87:00.0: enabling device (0000 -> 0002)
kern  :info  : [  293.734427] nvme nvme6: 255/0/0 default/read/poll queues

kern  :info  : [  296.227642] pcieport 0000:86:04.0: pciehp: Slot(31): Card 
present
kern  :info  : [  296.355148] pci 0000:88:00.0: [1344:51c3] type 00 class 
0x010802 PCIe Endpoint
kern  :info  : [  296.355199] pci 0000:88:00.0: BAR 0 [mem 
0x00000000-0x0003ffff 64bit]
kern  :info  : [  296.355257] pci 0000:88:00.0: ROM [mem 0x00000000-0x0003ffff 
pref]
kern  :info  : [  296.355275] pci 0000:88:00.0: Max Payload Size set to 512 
(was 128, max 512)
kern  :info  : [  296.355438] pci 0000:88:00.0: PME# supported from D0 D1 D3hot
kern  :info  : [  296.355543] pci 0000:88:00.0: 8.000 Gb/s available PCIe 
bandwidth, limited by 2.5 GT/s PCIe x4 link at 0000:86:04.0 (capable of 63.012 
Gb/s with 16.0 GT/s PCIe x4 link)
kern  :info  : [  296.355977] pci 0000:88:00.0: Adding to iommu group 41
kern  :info  : [  296.359042] pcieport 0000:86:04.0: ASPM: current common clock 
configuration is inconsistent, reconfiguring
kern  :info  : [  296.362046] pcieport 0000:86:04.0: bridge window [io  
0x1000-0x0fff] to [bus 88] add_size 1000
kern  :info  : [  296.362072] pcieport 0000:86:04.0: bridge window [io  size 
0x1000]: can't assign; no space
kern  :info  : [  296.362079] pcieport 0000:86:04.0: bridge window [io  size 
0x1000]: failed to assign
kern  :info  : [  296.362086] pcieport 0000:86:04.0: bridge window [io  size 
0x1000]: can't assign; no space
kern  :info  : [  296.362090] pcieport 0000:86:04.0: bridge window [io  size 
0x1000]: failed to assign
kern  :info  : [  296.362097] pci 0000:88:00.0: BAR 0 [mem 
0xd4500000-0xd453ffff 64bit]: assigned
kern  :info  : [  296.362119] pci 0000:88:00.0: ROM [mem 0xd4540000-0xd457ffff 
pref]: assigned
kern  :info  : [  296.362125] pcieport 0000:86:04.0: PCI bridge to [bus 88]
kern  :info  : [  296.362133] pcieport 0000:86:04.0:   bridge window [mem 
0xd4500000-0xd45fffff]
kern  :info  : [  296.362140] pcieport 0000:86:04.0:   bridge window [mem 
0x1e6000200000-0x1e60003fffff 64bit pref]
kern  :info  : [  296.362653] nvme nvme7: pci function 0000:88:00.0
kern  :info  : [  296.362672] nvme 0000:88:00.0: enabling device (0000 -> 0002)
kern  :info  : [  301.227714] nvme nvme7: 255/0/0 default/read/poll queues

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https://bugs.launchpad.net/bugs/2100828

Title:
  ubuntu-24.04: Root port link speed degradation to 2.5GT/s after nvme
  hot plug

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