Since this is your first post I'll assume your a newbie and start at the beginning. It sounds like the very common air in the fuel manager head problem and they are hard to find but share common areas. This can be as simple as a loose hose clamps, there are three, two on the fuel manager and on the high pressure fuel pump. The system is under a vacuum so you won't see fuel leaking out other then from a burnt heater plug on the fuel head. That's the one with that has the red and black wires, remove it and if there's diesel fuel inside there you've found it. Wait three weeks for another

A good service tech should already have checked the filter for water, replaced the filter and reprimed the system but don't "assume"

Still have a problem

Drop the tank and check for debris clogging the intake screen on the bottom of the pickup basket as mentioned. Worst case is your high pressure pump has a problem. You didn't mention if it threw any codes or not.
If you hear a "whoshing" sound have them check the intake hoses for slits. Look for oil spots that are tell tale sign. Don't overlook inside the plastic screen type stuff. But it does sould like a fuel problem.
Most 05 and 06 CRD's suffer from some type of air in the fuel problem and an in tank cummins lift pump is the ultimate solution for it
Since you said "500kms" I'll assume your not from the US but maybe Canada. Most US dealers techs don't seem to know much about our CRD's and their Mexican counter parts sound like the same

We really should not expect much from a gasser tech who was given half a day instructions on diesels
To test your MAF (Mas Air Flow, is this what they replaced) you could unplug it, you'll get a cel but under normal situations it will run better.
There is also a problem on 06 models where the engine wiring harness is rubbing on the bracket holding the fuel filter head causing shorts and intemittent problems. On 05's the harness is routed a few inches lower.
You didn't mention your total mileage (KMS) but if your out of warranty or really desperate find a decent independent diesel mechanic.
Good luck
Joe