Hi I have a peugeot 206 1.9L Diesel (1999). I recently changed the fuel filter and now the engine is running very rough and sometimes cutting out especially at low speeds. I have noticed that there is lots of tiny air bubbles in the fuel line between the fuel filter housing and the fuel pump. Is it likely that these air bubbles are causing the running problems and if so how can i fix the problem please ?
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If the bubbles are in the fuel line that leads to the high pressure pump, then air in the system would reduce the pumps ability to pressurise the fuel correctly. Diesel injectors require high pressure fuel in order to achieve proper atomisation; liquids don't burn, so the fuel needs to enter the cylinder in very fine droplets in order for a clean burn to occur.
I assume that you filled the filter housing with diesel during the filter replacement procedure? Otherwise there will be air in the system.
The system also needs to be correctly primed so that fuel reaches the high pressure pump correctly. This is usually done by a hand pump or by one that is attached to the filter body.
Check for leaks around the filter. Also check all the lines and connections and make sure that the fuel filter has been fitted correctly. I believe these engines use a paper filter which you insert in to a housing (I've only experienced the Peugeot 1.9 diesel engine on a van, so the car variant may be different) - you may want to make sure that the housing has been put back together correctly.
I have heard of issues with air getting trapped in the fuel solenoid (which I believe to be attached to the high pressure pump), for example:
"The diesel solenoid was taken out and the hand bulb primer given a good squeeze which seemed to clear a blockage." (http://www.peugeotforums.com/forums/vans-16/stumped-boxer-1-9d-not-starting-18487/)
If this doesn't work, and because the poor running has occurred immediately following a change of fuel filter, it may be wise to acquire a set of second hand fuel hoses and filter housing from a scrap dealer to see if that resolves the issue (as you may have damaged the housing, line or one of the connections whilst changing the filter).
If I am wrong and the fuel filter is a complete replacement unit, then make sure you have a high quality filter (bosch / delphi etc) from a reliable parts supplier. If you haven't then I recommend fitting one as, in my experience, a cheaply made fuel filter can cause diesels to run poorly.