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I have been out of the VW scene for a long time, but from my (probably now ancient) experience with the VW MkIV 1.8T cars, I'd say an ECU tune involving a VW to have the following effect:
1) Generally, the core engine components (on a VW) are very stout, and big name ECU tuners know their stuff well enough that their tunes are almost always very safe (as far as long term reliability is concerned). However, accessory components may see accelerated wear / failure rates and require more frequent replacing / upgrading -- think valves and piping here.
On top of that, early tunes -- ie. those that are released soon after the car became available -- tend to need a bit of time to mature and get everything right. Given your car is a B7 2.0T, that engine has been around for a LONG time, so I don't anticipate any major issues for you. Still, I'd watch out for boost spikes.
2) IMO, you can't go wrong with APR. They are not the only reputable game in town, but in the VW scene, you really can't go wrong with APR. GIAC is potentially another option, and I used to like Neuspeed as well.
3) As far as turbo upgrades are concerned, I'm gonna ask you this -- what is your intended purpose of the car? Big turbos and their big numbers are certainly attractive on paper and important for bragging rights, but unless you plan on regularly tapping into that potential (eg. lapping days?), I might just actually prefer the stock K03 instead. The K03 has its charms with lower revs quick spooling. Yes, it runs out of breathe at the high end, but for stints around town and quick jabs on the freeway to overtake someone, I have to say I like the K03 more.
When I first looked into chip tuning in the early 2000's, I think the area was still in its infancy -- it was definitely nowhere nearly as popular and convenient as it is now. At the time, most tuners require you to pay again, albeit at a discounted rate, for re-tunes when you add new performance parts. Updates for the same level of tune has generally been free though. Nowadays, most, if not all, of the ECU tuners that I am familiar with offer lifetime remote updates and fine tuning. They specifically advertise themselves to cater to your gradual upgrades as well, so that you'd can get the most out of any new engine parts you install. Unfortunately, I am no longer familiar with APR, so I don't know what their current tuning update policy is. Best to fire them a quick email to check.
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