When you delete a problem from a set, you have two choices. If I were to delete #2 from a set with #1,#2,#3, I can either leave the remaining questions as #1,#3, or renumber to #1,#2.
If you leave them as #1,#3, this will break a Gateway Quiz, which needs the assigned problems to come in a regular order. (That is perhaps a design flaw that could be corrected with some investigation.)
If you change them to #1,#2, that won't change the history of each student's actions with the original #2 and #3. For example, if they had already answered #3 correct, the database says they have score 1 for #3 (but now ignores that). And now the database may still say they have score 0 for #2 because they never answered the original #2 correctly. They may need to resubmit an answer for the new #2. I may not have gotten that quite correct, but things similar to this will happen. So deleting a question and renumbering is not advised unless you are sure no students have worked on the problem set yet.
Lastly, changing something about the parent Gateway assignment might have no effect on individual versions of a Gateway problem set that has already been started. You would have to visit each particular version if you wanted to make real changes.
As Danny says, marking the question correct of everyone is a good option. (Although, do you have to do that for each version?) At the same time, you might set the weight of the question to 0 so that it doesn't artificially raise everyone's score.