If cfrogue wants some more detailed math, here it is:
Say that in the launch frame, the left ship is at position x=0 at time t=0, and the right ship is at position x=d at time t=0. At t=0 they both begin to accelerate with constant coordinate acceleration a in the launch frame, and they both stop accelerating at time t=t1 in the launch frame. Then prior to t1, v(t) for both ships will be given by v(t) = a*t, and x(t) for the left ship will be given by x(t) = (1/2)*a*t^2 while x(t) for the right ship will be given by x(t) = (1/2)*a*t^2 + d. So at time t1 when they stop acceleration, both ships will have a velocity in the launch frame of a*t1, and the position of the left ship will be (1/2)*a*t1^2 while the position of the right ship will be (1/2)*a*t1^2 + d. After that they both move at constant velocity v1 = a*t1, so after t1 x(t) for the left ship will be given by x(t) = v1*t - v1*t1 + (1/2)*a*t1^2 while x(t) for the right ship will be given by x(t) = v1*t - v1*t1 + (1/2)*a*t1^2 + d.
Now we can use the formula I derived in
post 134 of the twins thread, which tells us that if we pick the event E of the left ship stopping acceleration, and pick another event E' on the worldine of the right ship which is simultaneous with E in the ship's own inertial rest frame, in the launch frame where the right ship is moving at speed v1 and was at a distance of d from E when it happened, the coordinate time between E and E' must be (d*v1/c^2)*gamma^2, so if E occurred at time t1, E' occurred at time t = t1 + (d*v1/c^2)*gamma^2. Plugging this time into the x(t) for the right ship, E' must have occurred at a position of x = v1*[t1 + (d*v1/c^2)*gamma^2] - v1*t1 + (1/2)*a*t1^2 + d = (d*v1^2/c^2)*gamma^2 + (1/2)*a*t1^2 + d.
So, coordinates of E in the launch frame:
x = (1/2)*a*t1^2, t = t1.
Since v1 = a*t1, the coordinates of E can be rewritten as:
x = (1/2)*v1*t1, t = t1
Coordinates of E' in the launch frame:
x = (d*v1^2/c^2)*gamma^2 + (1/2)*a*t1^2 + d, t = t1 + (d*v1/c^2)*gamma^2.
Since v1 = a*t1, the coordinates of E' can be rewritten as:
x = (d*v1^2/c^2)*gamma^2 + (1/2)*v1*t1 + d, t = t1 + (d*v1/c^2)*gamma^2
And remember, E was an event on the worldline of the left ship--the event of it stopping its acceleration--and E' was an event on the worldline of the right ship--the event that happened simultaneously with E in the right ship's inertial rest frame once it finished accelerating. So, now we can figure out the x' and t' coordinates of E and E' in the rest frame of the ships after they stop accelerating, using the Lorentz transformation, and the difference in x' coordinates of the two events will be the distance between the ships in their final inertial rest frame once the left ship stops accelerating.
The coordinates of E in the ship's final inertial frame are:
x' = gamma*((1/2)*v1*t1 - v1*t1) = gamma*(-1/2)*(v1*t1)
t' = gamma*(t1 - (1/2)*t1*v1^2/c^2)
The coordinates of E' in the ship's final inertial frame are:
x' = gamma*([(d*v1^2/c^2)*gamma^2 + (1/2)*v1*t1 + d] - v1*[t1 + (d*v1/c^2)*gamma^2])
= gamma*(d + (-1/2)*v1*t1)
t' = gamma*([t1 + (d*v1/c^2)*gamma^2] - v1/c^2*[(d*v1^2/c^2)*gamma^2 + (1/2)*v1*t1 + d])
= gamma*(t1 + gamma^2*(d*v1/c^2)*[1 - v1^2/c^2] + (-1/2)*t1*v1^2/c^2 - d*v1/c^2)
= gamma*(t1 + [1/(1 - v1^2/c^2)]*(d*v1/c^2)*[1 - v1^2/c^2] - (1/2)*t1*v1^2/c^2 - d*v1/c^2)
= gamma*(t1 - (1/2)*t1*v1^2/c^2)
So, you can see here from direct calculation that both E and E' do have the same t' coordinate in their final rest frame, regardless of whether you trusted my derivation in post 134 of the twins thread. You can also see that the difference in x' coordinate between E and E' is gamma*d, so this must be the distance between the two ships in their final rest frame, which is greater than the distance between them in the launch frame by a factor of gamma.