My initial problem was that BIP0039 is not backward compatible with Electrum. When trying to solve that, I realized that the seed encoding used in Electrum does not help, because it does not contain a version number information. However, BIP0039 suffers the same shortcoming: it does nothing to help a future replacement, it wants to be final. My first recommendation is to allocate a few bits of the mnemonic, in order to encode a "version number" along with the checksum bits.