What should I do if I miss the deadline to file a lien

How much were you shortchanged? For most residential work in NJ, you will not be able to properly allege claims under the NJ Prompt Payment Act. If the project was a single house, you would fall short of the minimum of six units needed to qualify. However, if you are owed a substantial sum it may still be worth your while to sue for breach of contract, unjust enrichment, etc. Please reach out if you would like to talk about your options.