In case you wanted $Y$ to be defined as follows:
$$
X_i \sim N(\mu_i, \Sigma_i) \; \text{for} \;i={0,1}
$$
so that
$$
Y = (X_0-\mu_0)'\Sigma_0^{-1}(X_0-\mu_0) \; - \; (X_1-\mu_1)'\Sigma_1^{-1}(X_1-\mu_1)
$$
where the subtrahend and minuend both are $\sim \chi^2(n)$. I therefore assume that both $X_i$ follow a $n$-variate normale distribution and that $X_0$ and $X_1$ are independent.
Then the difference $Y$ follows the variance-gamma distribution. There was already a similar question to this problem in the math community on stackexchange:
Transformation of Difference of Random Variables
In R you can verfiy the result you find following the above link via the following code chunk:
library(MASS)
library(VarianceGamma)
sigma0 <- diag(4)
sigma1 <- diag(4)*2 + 1
X0 <- mvtnorm::rmvnorm(50000, mean=rep(0, 4), sigma0)
X1 <- mvtnorm::rmvnorm(50000, mean=rep(0, 4), sigma1)
X <- cbind(X0, X1)
Y <- apply(X, 1, function(z) { t(z[1:4])%*%solve(sigma0)%*%z[1:4] - t(z[5:8])%*%solve(sigma1)%*%z[5:8] } )
truehist(Y, nbins = 50, ylim=c(0,0.2))
lines(x=seq(-20,20,0.01)-4, y=dvg(x=seq(-20,20,0.01), vgC=4, sigma=4, theta=0, nu=0.5))
