What is a "legend?"
According to the Merriam-Webster dictionary a legend is...
a
: a story coming down from the past;
especially
: one popularly regarded as historical although not verifiable
- the legend of a lost continent
- Arthurian legends
b
: a body of such stories
- a place in the legend of the frontier
c
: a popular myth of recent origin
- the legend of the Loch Ness monster
So keep all this in mind with the Legend of Zelda series if you are trying to scramble your brain to fit together the chronology of two events that just do not fit. You may be able to come up with alternative explanations, but this is the most simple way to explain it and not rack your brain unless you really want to. We have a base outline of the series from the official canon, but all the little details in the games may cause a bit more confusion if you're really looking that closely. Zelda is a great tale, but not everything is perfected.