Took over new client and the last 2 years the CPA filed 1120S under wrong EIN number - first off don't know how - second how do you correct if the IRS doesn't send letters?

Personally, I would amend the Form 1120S returns with the correct EIN, to get the records straight if for no other reason.

You can also go over the 2015 and 2016 returns with a fine-tooth comb and make any corrections you deemed necessary.