OK, it seems that the actual problem was that --export-secret-subkeys does not work if I leave the passphrase empty. Since my hard disks are encrypted, I usually do not have passphrases for my secret keys and since GnuPG 2.0 this created some problems. When I exported them with a passphrase and imported them, giving that passphrase, they are correctly merged into the existing key. Afterwards the passphrase can be deleted again. I now also understand why gnupg is always asking multiple times for a (new) passphrase when exporting or changing the passphrase - it seems to have a different passphrase for each subkey. Of course this is not very helpful if the dialog does not specify which key is about to be changed. I guess I should file a bug report for this, if I create a new subkey every year it will take quite a while to export the complete key if I have to type a passphrase for each of them in a few years...
Thanks, Viktor
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