In the BC1: Tales of the Toa, The Shadow Toa were defeated by the Toa Mata by changing the opponents which was considered non-canon because of the Encyclopedia.
In the Encyclopedia, the Shadow Toa were simply defeated by absorbed by the Toa Mata.
Couldn’t it be possible that after the Toa defeated the Shadow Toa as Hapka wrote in the BC1, the Shadow Toa reappeared and were absorbed as it’s written in the encyclopedia? Meaning that both versions are canon and Hapka’s battle description could be a prequel to the final ending of the Shadow Toa and the final confrontation with Teridax? the same thing happened in the Manas fight (MNOG - Hapka book mixture).