Spoiler
The evil of Echo took advantage of his need to seek the truth, in the end he became Socket man and began to, sort of, travel through time. Every time you see Socket man, well.... That's Flynn....
spoiler
Ok, let me recapitulate a bit (I may be a little bit off tracks 'cause I only went through it once.
He went to the mines, got burned, saw all echo, somehow got transported back when salamander boy saw him and he tried to rescue him, then got taken to the lake and that's when TJ saw him just before what happened to Sydney, then got transported waaaay back when Carl's ancestor pinned his crimes on his lover and his lover got hanged. Basically the evil was just transporting him here and there taking his conscience, Flynn sometimes remembering who he was, but mostly was not in a sort of auto-pilot. At least that is what I gathered. Don't know if that answers....a bit at least haha.