"In past years if all 1099s weren't reported in a client's tax return, because they didn't submit all of them, they received a letter from the IRS stating that they had unreported income and were assessed additional tax, penalty and interest."

If all the income that had been reported to IRS on 1099s wasnt included on the Sch C, yes, you'll get a CP2000 for missing income, but its not due to individual 1099s not being entered, its due to the total income not matching IRS records.

Your clients need to reporting ALL income their business received, they should be keeping track of this themselves (thats what businesses do!) regardless if they received a 1099 or not.