Hi there,
I have a Thinkpad X390 and Fedora 38 with GNOME. The laptop works perfectly besides Thunderbolt. I never noticed it until I tried using it with a HDMI-connected display via Thunderbolt Dock.
The display now only gives me a 30Hz refresh rate which is surprisingly unusable. But this laptop does not support 4k@60Hz in any other way but through Thunderbolt.
Just to get some things out of the way: I can use the USB-C ports fine for USB things. I used a HDMI cable that supports 4k@60Hz, I just bought another one and both work with another laptop. I used proper Thunderbolt docks (adapters, docks from Caldigit). I played around with BIOS settings, updated firmware and even tried reinstalling Thunderbolt firmware and downgrading, etc. I am using the right port 
Which is the one used for the Lenovo dock but I also tried the other USB-C port in my desperation.
When I run lspci | grep Thunder I get:
02:00.0 PCI bridge: Intel Corporation JHL6240 Thunderbolt 3 Bridge (Low Power) [Alpine Ridge LP 2016] (rev 01)
03:00.0 PCI bridge: Intel Corporation JHL6240 Thunderbolt 3 Bridge (Low Power) [Alpine Ridge LP 2016] (rev 01)
03:01.0 PCI bridge: Intel Corporation JHL6240 Thunderbolt 3 Bridge (Low Power) [Alpine Ridge LP 2016] (rev 01)
03:02.0 PCI bridge: Intel Corporation JHL6240 Thunderbolt 3 Bridge (Low Power) [Alpine Ridge LP 2016] (rev 01)
04:00.0 System peripheral: Intel Corporation JHL6240 Thunderbolt 3 NHI (Low Power) [Alpine Ridge LP 2016] (rev 01)
3a:00.0 USB controller: Intel Corporation JHL6240 Thunderbolt 3 USB 3.1 Controller (Low Power) [Alpine Ridge LP 2016] (rev 01)
And I see the Thunderbolt controller in GNOME Firmware:
But in the settings I don’t see Thunderbolt as an option:
boltctl list does not show anything. When I run boltctl monitor I just get this
Bolt Version : 0.9
Daemon API : 1
Client API : 1
Security Level: user
Auth Mode : enabled
Ready
I tried several different auth modes in bios, even disabled security as much as I can (and allowed Thunderbolt during pre-boot, etc.) but no luck. If anyone has golden BIOS settings for this laptop I would be very thankful though.
I had the same issues on a previous Arch installation so I don’t think it is a Fedora specific issue, more a laptop-linux config? I hope I am not affected by this permanent thunderbolt bricking bug. I don’t think so because I don’t have many of these symptoms (USB-C not working, no HDMI via USB-C, no Thunderbolt in device tree, error messages, not charging, etc.).
Any help is much appreciated!