Hello Steven,

I think that there are two problems:
 - The Kernel does not notice that the device is gone.
 - The first hotplug operation, after removing a coldplugged device fails.

For the first one could you check whether thie pciehp (sub)-driver is loaded?
(dmesg | grep pciehp should show something, the config option is
CONFIG_HOTPLUG_PCI_PCIE).

I was able reproduce the second problem on my machine. Could you test whether
this patch fixes the problem?

Thanks,
Andreas

---
 drivers/thunderbolt/path.c | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/drivers/thunderbolt/path.c b/drivers/thunderbolt/path.c
index 8fcf8a7..9562cd0 100644
--- a/drivers/thunderbolt/path.c
+++ b/drivers/thunderbolt/path.c
@@ -150,7 +150,26 @@ int tb_path_activate(struct tb_path *path)
 
        /* Activate hops. */
        for (i = path->path_length - 1; i >= 0; i--) {
-               struct tb_regs_hop hop;
+               struct tb_regs_hop hop = { 0 };
+
+               /*
+                * We do (currently) not tear down paths setup by the firmeware.
+                * If a firmware device is unplugged and plugged in again then
+                * it can happen that we reuse some of the hops from the (now
+                * defunct) firmeware path. This causes the hotplug operation to
+                * fail (the pci device does not show up). Clearing the hop
+                * before overwriting it fixes the problem.
+                *
+                * Should be removed once we discover and tear down firmeware
+                * paths.
+                */
+               res = tb_port_write(path->hops[i].in_port, &hop, TB_CFG_HOPS,
+                                   2 * path->hops[i].in_hop_index, 2);
+               if (res) {
+                       __tb_path_deactivate_hops(path, i);
+                       __tb_path_deallocate_nfc(path, 0);
+                       goto err;
+               }
 
                /* dword 0 */
                hop.next_hop = path->hops[i].next_hop_index;
-- 
2.0.4

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