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Solution:
From IBM support.
For the 8.5.3 upgrade. Create a MST-file with the EXACT same lines in same order (as the old 8.5.2 mst file). And now the upgrade works. But only using this MST, if I am using the default install (no customized mst) the the port disappears again.
Feedback response number WEBB8NXM6T created by ~Tate Kikigengon on 11/25/2011