OK we've ruled out two obvious issues, now i'm no expert on these engines but isn't this the one fitted with a balance shaft and didn't that give trouble over time? maybe worth reading up on that engine in make specific forums, could be any of the VW makes who used that engine.
Alternatively it might be time to let a VW specialist or good Diesel workshop take a listen, in case it's something developing inside which might be fixable before it causes serious damage, for Diesel workshops taxi drivers who haven't yet dumped Diesels in favour of Toyota hybrids are the chaps to ask, sadly in my area the one brilliant go to place closed down many years ago after the boss retired and the company who took the name so far do not appear to be in the same league.
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