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Hello, I would be looking to check the condition of the fuel sender unit in the diesel tank, if the pick up is deteriorated and cracked, with a low enough fuel level, it will drag air into the system as it's sucking the diesel out of the tank.
I had a car that wouldn't run under half a tank due to issues with the pick up.
You could fill the tank to see if this eradicates the air, hence pointing to the pick up.
Next I would be looking to vacuum test the fuel lines from the sender unit to the engine to look for leaks, block the pipe at the pick up and apply vacuum at the filter connection using a mitty vac or similar.
If this comes back ok I would be vacuum testing the fuel filter and housing to check for leaks.
Next I would test the lines from the filter to the pump.
By this point I would expect you have found the issue.