Is the EGR cooler problem on my Skoda Yeti linked to the emissions fix?

I have a Skoda Yeti 2.0-litre diesel, bought in March 2012 . The Skoda garage performed the software update to correct the Volkswagen diesel emissions issue. About 6 weeks since change the car has developed a problem with EGR cooler mechanism. The price of parts and labour is about £1100. Is there a connection between the engine fix and the EGR as both are about nitrogen oxides. Are you aware of others experiencing this problem? Skoda may pay for parts but not labour.
This is too common for there not to be any connection. Basically the software remap makes the EGR cooler work harder, so if it is already partially clogged it rapidly gets worse. Yes, lots of other reports of precisely this problem, though more prevalent on the EA 189 1.6 TDI.
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