Have you got any code to show us how you are going through the array "randomly" ? I would suggest that you create an array of equal size of type boolean, set them all to false, and as you read a value from the first array you set the same element in the second array to true, which leaves you with some falses.
One question that you need to clarify is how many values do you collect?
If you pick up all randomly, you just need to sort and check the length of the random array, after that to find exactly which values are missing you just compare the random value with index x with the value from the source array at index x. If the values are equal, move to the next value.
If you pick up less than 100 values, lets say n values, you keep track of the number of times you pick up values, you will be able to see if there missing values, but you won't be able to know which ones.
Best regards