This is mainly a performance questions. I have a master list of all users existing in a String array AllUids. I also have a list of all end dated users existing in a String
Don't use arrays for this, use Collection and the removeAll() method. As for performance: unless you do something idiotic that leads to O(n^2) runtime, just forget about it. It's premature optimization, the useless/harmful kind. "thousands of users" is nothing, unless you're doing it thousands of times each second.
BTW, PHP "arrays" are in fact hash maps.