Typically in F# instead of using generic workflows you define the workflow by hand, or use one that is ready available as in your case async and maybe but if you want to use them combined you will need to code a specific workflow combination by hand.
Alternatively you can use F#+ which is a project that provides generic workflows for monads, in that case it will be automatically derived for you, here's a working example, using your workflow and then using OptionT which is a monad transformer:
#r "nuget: FSharpPlus, 1.2"
open FSharpPlus
open FSharpPlus.Data
let doAsyncThing = async {return System.DateTime.Now}
let doNextAsyncThing (x:System.DateTime) = async {
    let m = x.Millisecond  
    return (if m < 500 then Some m else None)}
let f x = 2 * x
// then you can use Async<_> (same as your code)
let run = monad {
    let! x = doAsyncThing
    let! y = doNextAsyncThing x
    match y with
    | None   -> return None
    | Some z -> return Some <| f z}
let res = Async.RunSynchronously run
// or you can use OptionT<Async<_>> (monad transformer)
let run' = monad {
    let! x = lift doAsyncThing
    let! y = OptionT (doNextAsyncThing x)
    return f y}
let res' = run' |> OptionT.run |> Async.RunSynchronously
The first function has to be 'lifted' into the other monad, because it only deals with Async (not with Option), the second function deals with both so it only needs to be 'packed' into our OptionT DU.
As you can see both workflows are derived automatically, the one you had (the async workflow) and the one you want.
For more information about this approach read about Monad Transformers.