Brain Potter, a good point you noticed.
A quick answer which comes to my mind
Quote from my post
That`s why ECAM steps always reliable at very complex cases resulted from combined failures, which normally pilot cannot do simply as reading from FCOm 3.02
In your scenario, probably
FCTL FLAPS FAULT/LOCKED ECAM willl also display, so when calculating Vapp you have to consider its effect as well.
But in any case, since the Vls always represents actual configuration, on the final if you see a Vapp above Vls your speed calculation is correct. If not, this means your speed calculation is wrong. Then simply fly a speed above Vls.