How to hide navigation Toolbar icon in xamarin?

Putting @Gerald answer in action, it would be done this way:

void Done_Clicked(System.Object sender, System.EventArgs e)
{
    //Do somthing and hide the done item
    ShowDoneToolbarItem(false, (ToolbarItem)sender);
}

void Entry_Focused(System.Object sender, Xamarin.Forms.FocusEventArgs e)
{
    //Show the done item
    ShowDoneToolbarItem(true);
}

void ShowDoneToolbarItem(bool show, ToolbarItem item = null)
{
    if(show)
    {
        ToolbarItem done = new ToolbarItem();
        done.Text = "Done";
        done.Clicked += Done_Clicked;
        ToolbarItems.Add(done);
    }
    else if(item != null)
    {
        ToolbarItems.Remove(item);
    }
}

This is cleaner and works from the code behind.

I would suggest to build a bindable ToolBoxItem. That way you can control the visibility through a view model property.

An implementation could look like that:

public class BindableToolbarItem : ToolbarItem
{
    public static readonly BindableProperty IsVisibleProperty = BindableProperty.Create(nameof(IsVisible), typeof(bool), typeof(BindableToolbarItem), true, BindingMode.TwoWay, propertyChanged: OnIsVisibleChanged);

    public bool IsVisible
    {
        get => (bool)GetValue(IsVisibleProperty);
        set => SetValue(IsVisibleProperty, value);
    }

    private static void OnIsVisibleChanged(BindableObject bindable, object oldvalue, object newvalue)
    {
        var item = bindable as BindableToolbarItem;

        if (item == null || item.Parent == null)
            return;

        var toolbarItems = ((ContentPage)item.Parent).ToolbarItems;

        if ((bool)newvalue && !toolbarItems.Contains(item))
        {
            Device.BeginInvokeOnMainThread(() => { toolbarItems.Add(item); });
        }
        else if (!(bool)newvalue && toolbarItems.Contains(item))
        {
            Device.BeginInvokeOnMainThread(() => { toolbarItems.Remove(item); });
        }
    }
}

As you have discovered yourself there is not IsVisible. So you will have to implement functionality like that yourself if you still want it.

Another way would be to handle it in the pages' code-behind and remove or add the toolbar item whenever needed.

Adding and removing is simple, just add and remove items to the ToolbarItems collection: ToolbarItems.RemoveAt(0); for instance will remove the first toolbar item.