What is the model of your LattePanda V1 board? You can see it on the sticker on the side of the female header.
Please ensure sufficient power supply, at least 5V 2.5A or above.

Also, could you try to see if similar issues occur in the Windows OS?

You can try:
Disable more power management related settings:
Disable C-states or other advanced CPU power management features
Disable USB selective suspend function
If there is a Runtime Power Management option, turn it off

In addition to the parameters already tried, add the following parameters to GRUB:

acpi=off
pci=noaer
pci=nocrs
acpi_osi=Linux acpi_osi=! acpi_osi="Windows 2009"

Also, what is the model of your Thunderbolt to PCI board?

Complete design drawings and documentation are available in the GitHub repository at: https://github.com/LattePandaTeam/LattePanda-Mu/tree/main/Electricals/Examples/%5BDFR1142%5DLite%20Carrier%20for%20LattePanda%20Mu

Each component has detailed parameters and purchase links, and you can export a complete BOM yourself.

The mating connector for the Mu is: TE 2309411-1 H8.0 STD DDR4 SODIMM

Please confirm that your hard drive is a GPT partition, not MBR.

You can try using the Windows installation disc to repair the bootloader. The method is to start the computer with the installation disc, and then select "Repair your computer" instead of installing the system.

What is your SSD model? Generally, most commercially available M.2 SSDs that support NVMe can be used.

Which LattePanda board are you using?

M.2 B key slot can only be inserted into M.2 LTE wireless modules. 

For M.2 Wifi modules, an M.2 E key slot is required. If you want to connect an M.2 Wifi module, please insert the module into the M.2 E key slot.

I haven't encountered this problem using the Ugreen Type C HUB.

What is the model of your Type C HUB? Can you provide a link? 

Did you install your operating system yourself, or are you using the official image?

Please try the following methods to rule out hardware issues:
1. Use Windows 10 or 11.

2. Use another NVMe SSD.

Additionally, check the BIOS version and see if you can enter the BIOS interface to check if the ethernet device is present.

Which board are you using?

Try this method first: https://docs.lattepanda.com/content/sigma_edition/Operating_Systems_WinServer/#network-driver-installation

@Craig.Paterson4775  The M.2 E key on the lite Carrier only has PCIe signals and no CNVio signals, meaning it only supports WiFi modules that use PCIe communication.

Therefore, Intel AX201 and AX211, which use CNVio communication, cannot be recognized. You can use Intel AX200 or AX210 WiFi modules instead.

Glad this post was able to help you ^_^

When the RTC battery has sufficient power, the board can automatically power on when connected to a power source because you set ACPowerLoss to "Power On" in the BIOS. 
However, when the RTC battery is low, this setting will not work, and you will need to short the SW and AUTO pins.

Therefore, to ensure the reliability of the automatic power-on feature, both of the above settings are necessary.

Please try using this method to reflash the BIOS firmware: https://www.lattepanda.com/forum/topic/336081

If the issue persists, it is likely a hardware failure. Please contact techsupport@lattepanda.com for repair services.

The PCIe lanes for the ethernet chips and M.2 M key are independent and will not interfere with each other. 
Did you insert the SSD after shutting down and powering off the board? Also, could you let me know the model of your NVMe SSD? Is the SATA SSD functioning properly?

Near the power indicator, there is the pin header with white silk screen printed "PM," which includes status indicator pins like S0, S3, S4, and S5. 
You can test them to find the pin you need. Also, remember to connect the pins and LED with a resistor of at least 200 ohms to prevent the LED from burning out due to overvoltage.

Are you talking about USB audio devices? As long as it is a USB communication-based audio device, it can be used normally. Some devices may require installing the drivers provided by the manufacturer to work. 
Most of these devices use a USB A port. Devices on a USB C port do not affect the USB A port, because the signals of these two types of USB interfaces are completely independent.
 

An external GPU connected through a Thunderbolt dock can function normally. Of course, the operating system needs to have the GPU drivers installed.

The SPI pins of LattePanda Mu are only for the BIOS Flash chip and cannot be used for other devices. 
If SPI communication with other devices is needed, a USB conversion solution, such as the CH347 chip, can be used.

COM Port Allocation Mechanism in Windows:

When Windows detects a USB device, it assigns an available COM port number to it. If multiple USB devices have been connected to the system in the past, the port information for these devices is stored in the registry. When a device is reconnected, if the original port number is occupied, the system will assign a new port number.

Fixing COM Ports through Windows Device Manager:

Open Device Manager.  
Locate the Arduino device (under "Ports (COM & LPT)").  
Right-click on the device and select "Properties."  
Click on the "Port Settings" tab.  
Click on "Advanced."  
In the "COM Port Number" dropdown menu, select a fixed port number.  
Choose a larger number (e.g., COM20) to avoid conflicts with other devices.  
Click OK to save the settings.

Of course, it is recommended to improve your program to automatically search for devices containing "Arduino Leonardo" in their names, thereby automatically obtaining the corresponding COM port number.

If you have the code, you can compile and upload it directly using the Arduino IDE. 

Or are you saying you already have a compiled .hex file and want to directly upload it to the Arduino Leonardo?

Please first check the power adapter and try replacing it with another one. 

If the power supply is normal, you can try reflashing the BIOS firmware. Refer to this post: https://www.lattepanda.com/forum/topic/336081.

If the issue persists, hardware failure cannot be ruled out. Please contact techsupport@lattepanda.com for repair services.

Is your board the model that comes with an activation code? 

Additionally, please note that you need to run the software to get the activation code before reinstalling the OS.