set.seed(12345)
require(data.table)
dt <- data.table(col1 = rnorm(n=10, mean=20, sd=5), col2 = runif(10, 0, 1), col3 = rbinom(10, 3, .5),
             col4 = rnorm(n=10, mean=20, sd=5), col5 = runif(10, 0, 1), col6 = rbinom(10, 3, .5))
nas1 <- which(dt[,col1] %in% sample(dt[,col1], 3))
nas2 <- which(dt[,col2] %in% sample(dt[,col2], 4))
nas3 <- which(dt[,col3] %in% sample(dt[,col3], 2))

dt[nas1, col1 := NA]
dt[nas2, col2 := NA]
dt[nas3, col3 := NA]

cols.tochange <- c("col1", "col2", "col3")
.sdcols <- c("col4", "col5", "col6")

dt[, (cols.tochange) := .SD, .SDcols = .sdcols]