Sidenote: Your statement is only true if you know the initial value of states X_0. Otherwise, you cannot do a simple inversion.
Again, the answer is: it uses the Kalman filter (see e.g. Hamilton 1994: Time Series Analysis)
When there are missing values or more shocks than observables, it still holds that
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Y_t = A X_t-1 + B e_t
or
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Y_t-A X_t-1=B e_t
That is, the residual on the LHS follows a multivariate normal distribution. You can think about the solution being the "maximum likelihood estimate". For example, say that the residual for a variable is 2 and it is driven by two uncorrelated standard normal shocks. Then the solution should be that both shocks take on the value 1 as this is the most likely linear combination giving rise to a residual of 2. Another "solution" would be having one shock being 2 and the other being 0. But this is less likely:
normpdf(2)+normpdf(0)= 0.4529
normpdf(1)+normpdf(1)= 0.4839