Reading Fowler et al, there is something in regards to the intialisation of the surface code in a logical state (ie a state of a logical operator) that is confusing me.
I can think of two examples that illustrate my problem. The first is restricted to planar code. The initialisation of a logical $|0\rangle_{L}$ or $|+\rangle_{L}$ is performed by taking all the data qubits, initialising them as either $|0\rangle$ or $|+\rangle$, and then turning on the stabilisers.
In the case of $|0\rangle^{\otimes n}$, $\hat{Z_{L}} |0\rangle^{\otimes n} = |0\rangle^{\otimes n}$, showing it to be a +1 eigenstate. From here, initialisation proceeds by turning on all the stabilizers. The $\hat{Z}$ stabilizers shouldn't affect this state. So only the $X$ stabilisers will. However, $\hat{Z_{L}}$ commutes with all of them. So this means I can expand it as a linear combination of both +1 and -1 eigenvectors of the $\hat{X}$ stabilizers, correct? However, this means that, while an projection by the $X$ stabilizers will give a +1 eigenstate of $\hat{Z_{L}}$, only the projections
$$\frac{(I+\hat{X_{s}^{i}})}{2}$$
will give me a +1 eigenstate of $\hat{X_{s}^{i}}$, where $\hat{X_{s}^{i}}$ is a stabilizer that measures in the $X$ basis to identify $Z$ errors.
Looking at Fowler et al, in the section where they show how to initialize a +1 $\hat{Z_{L}}$ eigenstate, on page 17, they also say that after measuring the qubits initialized in a state of $\hat{Z_{L}}$ with 3 $\hat{X_{s}^{i}}$ stabilizers, we end up with an eigenstate of all the stabilizers. However, like before, the outcome being a +1 or -1 eigenstate of these $\hat{X_{s}^{i}}$ is random.
Since this is the case, what do we do here? We can't just use the -1 result and update the 3 stabilizers, or in the case of the planar code, however may gave a -1 result. This would result in a change of stabilizers that could affect other parity measurements, especially in the case of the surface code. For example, if I took the stabilizer being data qubits 1 and 2 in Fig.14 of Fowler et al, and changed it to $-\hat{X}$, wouldn't this affect the measurement results? Or is it the case that now it just means that the surrounding qubits are taken to a state that is a simultaneous +1 eigenstate of this new operator and the old ones.
Or do we just take this as a failed initialization attempt and try again?