I've just had the same problem on my VW Polo which is fitted with the same 3 cylinder 80ps TDI engine, (prefixed BNV) as some Fabias and Roomsters.
I've had the car from new and it has been properly serviced (although not by a main dealer) using VWs very expensive long life oil, as the car is set up for the long service interval. The car is 4 years old and has covered 50,000 miles.
The problem became apparent when the oil light illuminated immediately after the car had missed a beat at about 30mph. I stopped straight away and checked the oil level which was fine. I then had the car recovered to my local garage.
They stripped it down and diagnosed a broken oil pump chain and drive sprocket and subsequent damage to the associated tensioning gear. Their initial quote was for approx £500 depending on the exact cost of spares. Obviously I wasn't too pleased given the age and mileage of the car, but put it down to bad luck and decided to take it on the chin.
The garage called back after a couple of days to say that they had now got all the parts, with the exception of the crankshaft drive sprocket which VW no longer supplied (discontinued 2007).
This would now necessitate a new crankshaft requiring engine removal to fit (new quote £1,800).
I called VWs customer service to enquire why they were unable to supply an essential wear part for a four year old car. They could not give a reason for it's discontinuation but confirmed it was no longer available and a new crankshaft would be required. I asked for a contribution towards the work as this was a totally unsatisfactory situation.
Initially they implied that no contribution could be made as the car had not been main dealer serviced. (Contrary to European legislation I believe). They later realised this mistake and said that they would possibly consider a contribution if I took the car away from the original garage (at the time stripped down on the ramp), delivered it to a main dealer, paid an inspection fee and provided reciepts to prove that original VW parts had been used during all previous servicing. I said obviously I wouldn't have the parts reciepts, as the car had been serviced at a garage, but they said that was the requirement.
It appears that the original fault occured due to the sprocket which drives the oil pump chain, failing and rotating on the crankshaft, subsequently shearing gear teeth and breaking the chain.
This sprocket is fitted over the end of the crank and has 3 flats machined into its bore which mate up to 3 flats machined onto the crankshaft itself. The purpose of these flats is to align the crankshaft to a balancing shaft which is also driven via the oil pump chain. This balancing shaft needs to turn in time with the rest of the engine and as such it is vital that the shaft is correctly timed to the engine via the sprocket location on the crank.
I is my belief that this is possibly a design fault, and that is why the part is no longer available. (VW part No 045 105 209) 045105209
Skoda told me that they also no longer supply this part , although I think theirs had a different part number.
I wonder if your car did actually require a new short engine, or just a new sproket/ chain.
I can honestly say that up until this point the Polo is probably the best car I have ever had, but after VWs terrible service, I shall never buy another car from the VW group.
