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Okay, now I  have tried re-doing the "initialise root resonances" and it
does not make a difference. The last spin-systems are still not exported. 

Also I have tried to make sense of the way the first spin-systems are being
exported. So most C-1 -atoms are in a new spin-system and most of them are
being exported (not all), but some are not in a new spin-system and some of
these are exported and others are not. And adding them to a new spin-system
or removing them from the spin-system makes no difference in what is being
exported. Also some of the C-atoms are not exported and here there is also
no obvious pattern as to why. Some of these have their C-atoms assigned to
CO, CA or CB of that spin-system while others does not and again changing it
makes no difference in the exported files.