Board Thread:DC's Legends of Tomorrow discussions/@comment-9346948-20170405000405/@comment-24152851-20170408095129

Though main reason I don't think this is the last we'll see of Eobard is he's Barry's arch-enemy. His complete antithesis who needs to appear at least once per season to menace Barry, much like Malcolm for Oliver.

There's also the fact, there should still be a time remnant of him in the future who needs to become enemies with Barry in the first place, become Harrison Wells and cause all of season 1 to happen.

My money is on something happens to prevent Eddie from killing himself, thereby removing Eobard's time remnant status entirely.