I reproduced the failure using Ubuntu’s signed in-tree `atlantic` driver
on kernel `7.0.0-31-generic`. The external Marvell 2.5.16.0 DKMS driver
was not installed for this kernel and remained only in DKMS’s `built`
state.

During boot, Linux enumerated the JHL7440 bridges and xHCI controller
first and allocated their bridge windows. The AQC113 appeared
approximately 165 ms later. Its downstream bridge could not obtain the
required 5 MiB memory window, all AQC113 BAR assignments failed with `no
space`, and the in-tree driver failed to probe with error `-5`. The
Thunderbolt enclosure still appeared authorized at 40 Gb/s, but no
Ethernet interface was created.

Removing the complete JHL7440 PCI subtree and rescanning the empty
parent bus caused Linux to redistribute the bridge windows and assign
every AQC113 BAR. Ubuntu’s in-tree driver then bound successfully, and
`enp8s0` established a 10,000 Mb/s link without rebooting.

This rules out the external Marvell DKMS driver as the cause of the PCI
resource-allocation failure. The evidence points to a PCI/Thunderbolt
enumeration timing problem: the AQC113 appears after the initial bridge
resource allocation, and the automatic hot-plug path does not resize the
sibling bridge windows afterward. Testing continues with the in-tree
driver to determine whether the separate spontaneous Thunderbolt Link
Down also reproduces.

** Attachment added: "intree driver supplemental failure file"
   
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/2167202/+attachment/6000018/+files/intree-driver-failure.txt

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https://bugs.launchpad.net/bugs/2167202

Title:
  thunderbolt/pci JHL7440/AQC113 fails to recover after tunnel
  disconnect; BAR allocation fails

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