VAG diesel Turbos can fail big style (oil smoke, no performance etc.) but more usually they can show symptoms of overboost when they get clagged up. This also causes the occasional lack of performance you report. If it's been found on diagnostics, chances are it is the second option. A new turbo is the dealer's chosen fix, but you can strip it and clean out the carbon to get the turbo working again. I've done this successfully on an Audi.
If the car is still under warranty, just let them get on with it. They might not like your Bluefin though (if could even be the cause of a wrong reading at diagnostic), so it might be a good idea to take the car away, take out the Bluefin and give them car back for the work to be done. You can imagine the conversation, "we've fitted a new turbo sir, but your aftermarket mod is the cause of the problem so you owe us £2000".
If the car is not under warranty, do a search of TDiClub.com for info on turbo problems, how to diagnose and how to fix them. Also, ask the dealer exactly what fault codes it threw up and what they mean. A new turbo is the last and most expensive option if all else fails.
I hope this helps.