Suppose x contains the first series of observations and y contains the second series of observations, where there is a gap between them consisting of m time periods. Let z be the complete time series, given by
z <- ts(c(x,rep(NA,m),y), frequency=??, start=??)
I assume you will set the start and frequency to suitable values.
Then you fit the first model using
fit <- auto.arima(x)
After you have obtained the additional observations, you can update the model in several ways. First, you might just compute the residuals on the new observations without revising the parameters or model order:
fit1 <- Arima(z,model=fit)
Alternatively, you might not revise the model order, but you do update the parameter estimates. In that case:
fit2 <- Arima(z,order=fit$arma[c(1,6,2)])
(Here I have assumed it is a non-seasonal ARIMA model. For seasonality, you would need to add a seasonal argument.)
Lastly, you might revise both the model order and the parameter estimates. Then
fit3 <- auto.arima(z)