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Ok, I removed both ORIGINAL_EPUB and the current EPUB. Did the conversion again, and the table of contents was complete. I repeated for the two other odt files, and same result, it worked, table is complete.
As this worked, I don't know what the toc.ncx could contain, it has been erased. I can recover an older copy from the kobo touch device, though, if anyone is interested in investigating it. Or set the limit to 50, erase files, convert, back to 70 without erasing, see if the fault repeats.
As far as I'm concerned, problem is solved, thanks :-)
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