On our last Data Integrity Exam we had a loan that was secured by 20 properties that was reported 20 times and was not split up properly, therefore we had 20 incorrect entries to the LAR, which was obviously over the error threshold. I was just looking at our error ratio report from our examiner and she didn't even include the 20 errors. It could be the fact that there were so many other errors that she focused on the real errors as opposed to just this one loan. (Trust me, this Data Integrity Exam was a nightmare - I'd just started working with the bank and went into the exam just a few weeks later, and found out all of this fabulous info. They made us re-submit 2012, 2013 & correct all of 2014)
However - I would count each field on your missed loans or duplicated loans as an error, my rationalization for that is the fact that you're only going to get tested on 60 loans no matter how many loans you have submitted on your LAR. You can only have a 5% error ratio in "non-critical fields" (Every field except for application date, action date & income) or you cannot go above a 10% error ratio overall. So you can make only 3 errors in any one field or 6 errors overall. If you've missed 2 loans off your LAR, and duplicated 2 more, well you've got 4 errors in one field and that's over your threshold!
I may not be right but I'll be darned if my bank messes up another data integrity exam! Trust me, I'd rather be overly cautious on this especially with HMDA data leading into Fair Lending, and the reliance of this data for CRA.
Best of luck to you in your exam.
Can't is not an option.