Your clients will not get a notice if the 1099 amount is not shown on the return.  They are more likely to get a notice if an unexplained adjustment is shown on Schedule 1.  A little knowledge about the CP2000 program can go a long way.  Notices are not sent without operator review.  The matching program will show an IRS employee the source and amount of any discrepancy.  Even an IRS employee can identify that a 1099-MISC from Franchise Tax Board is "one of those," and move on to the next case.