Capital/Income Ratio in Pikketty's Capital
First, important thing to note here is that $K/Y$ is not the capital income to labor income ratio, but ratio of capital to total income (or output which is macro-economically equivalent to income). $K$ is not an income derived from capital it is the stock of capital. 

Wars destroy the stock of capital so even though returns to capital $r$ indeed increase the fall in the stock of capital makes the capital-income ratio fall.  

Furthermore, the share of income going to capital is according to Piketty given by $\alpha = r \frac{K}{Y}$, and hence even if the rate of return increases when capital becomes more scarce the actual share of income going to capital might decrease if the capital-income ratio falls sufficiently to offset an increase in $r$.