If all their Health and Welfare Benefits were encompassed in one plan, they would only be required to file one 5500, but all lines of coverage including those with less than 100 participates would still have to be reported. If the SPDs have not been combined then only the plans with more than 100 participants would require the filing of a 5500.
The Department of Labor does provide a program for delinquent filers, which is of voluntary compliance, and reduces the penalties, accrued for the delinquent filing. Please refer to the link below for more information about Delinquent Filer Voluntary Compliance program.
