The solution I found is to not use the make_subplots() function, and instead use the lower level API mentioned at the bottom of this page: Subplots in Julia
A MWE is then:
tr1 = scatter(;y=rand(5))
tr2 = scatter(;y=rand(10),yaxis="y2")
L1 = Layout(yaxis_domain=[0, 0.5], yaxis2_domain=[0.51, 1], yaxis2_anchor="x2")
p = plot([tr1,tr2],L1)
with the update step
tr2[:y] .= rand(10)
react!(p,[tr1, tr2],L1)