I am answering my own question.
It seems like the internal reference names are auto-generated every time you export a mission pack. I have managed to read the level names from the exported packs, and exporting my levels in reverse order (three, then two, then one) I was able to get the Set Next Level references correct. this means, however, that I can not export all three levels into one mission pack.
Auto-generated names also means that levels that are numbered, do not appear in a correct sequence in the mission list in Warfare Inc, as it seems levels are sorted by their internal reference names.
For a more elegant solution, I guess I will have to wait for the next release of the editor and hope that the problem is solved there.
