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This is an interesting question. For the most part visible bubbles are in the low pressure side of the fuel system as the plastic lines are not high pressure lines, and are not an indication of any potential trouble for the injection pump. In the high pressure side of the fuel system, those atmospheric bubbles will be collapsed and not noticed by either the pump or the injectors. If the engine starts fine, and runs fine, that is an indication that the high pressure side of the system is solid, at pressure. With enough air in the system at pressure to cause a problem for the longevity of the injection pump, I doubt the engine would run at all.
In my experience there is always a series of bubbles in the clear lines, they just don't fill the entire cross section of the insides of the lines at any particular point. When you say you have a leak, are you seeing Diesel leak out, or are you just concerned about these bubbles?
The flow rates of Diesel through the fuel lines is pretty slow in terms of feet per second or meters per second. Which means it is a task for the system to drag bubbles anywhere. If you want to try to eliminate the bubbles it might be good to take it out for an "Italian tune-up" and drive WOT up a hill for a few minutes to try to up the fuel flow rates. Someone more familiar with the routing of the lines may be able to provide a sequence to close them up or specific instructions for venting.
The owner's manual typically instructs you to crank the starter on these later models to clear the air in the lines after running out of fuel or opening the system and letting air inside. That is typically all I do, and once she fires up and runs smoothly, I ignore the little bubbles. Jim
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Own:
1986 Euro 190E 2.3-16 (291,000 miles),
1998 E300D TurboDiesel, 231,000 miles -purchased with 45,000,
1988 300E 5-speed 252,000 miles,
1983 240D 4-speed, purchased w/136,000, now with 222,000 miles.
2009 ML320CDI Bluetec, 89,000 miles
Owned:
1971 220D (250,000 miles plus, sold to father-in-law),
1975 240D (245,000 miles - died of body rot),
1991 350SD (176,560 miles, weakest Benz I have owned),
1999 C230 Sport (45,400 miles),
1982 240D (321,000 miles, put to sleep)
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