I assume that in non-COVID times, we might have seen Hain's debut.
As things stand though, England have no natural replacement for Root's role. Billings isn't really cut out for it and is more of a middle order batsman. The way I see it, England have two options...
Hand a debut to Livingstone at three. The fairly obvious decision and perhaps long overdue. He normally opens or else bats at four I believe but can do a job at three. He is more of a hitter than an accumulator though, so Root's absence will be felt there.
If Stokes is indeed not completely fit, play him as a specialist batsman at three. I've been calling for Stokes since his ban and return to bat higher in white ball cricket, he doesn't have the old ability to go after the bowlers from ball one and needs time to settle in. On the other hand, once settled he is extremely dangerous and can win games. He also has the ability to shift gears easily and can also knuckle down and build an innings if required even though the stats haven't showed it yet. Billings could then fill in the middle order.
I know Malan is a reserve and Morgan wants to have a look at the other players, but is it the worst idea to have him reprise his T20I role here? His domestic stats may not be flattering but unlike those T20 ones, his recent numbers are good and the overalls are affected by the earlier part of his career significantly. He can accumulate adequately and can also hit boundaries whenever needed. Wouldn't surprise me if they go to him if the series is on the line.