In practice, the subterfuge would be recognized the first time that a hand appears that shows two Ace of clubs. This will happen frequently, at which point you are 100% sure that the deck is altered.
In terms of the simulation, your situation is equivalent to using a deck of 52 numbers that look like this:
{1,1,2,3,4,6,7,8,...,52}, where '1'=AC and '5'=2C.
If you want to stick with your original problem, which estimates frequencies, I suggest you start with a smaller deck for which the simulation will run faster and for which the probabilities are larger. For example, start with a deck of 8 cards (Aces and Twos) that look like
{1,1,2,3,4,6,7,8}. Figure out the answer to your problem with this smaller deck. When you can solve the problem with a deck that has 8 cards, test your knowledge by moving to a deck that has 12 cards. Then try 16. Then you will be ready for 52.
It sounds like your problem is related to using simulation to estimate "power and sample size." See these articles:
What sample size do you need for a binomial test of proportions? - The DO Loop
Sample size for the Monte Carlo estimate of an integral - The DO Loop
Use simulation to estimate the power of a statistical test - The DO Loop
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