A loan that was supposed to be secured by a lien on a business ended up originated with incorrect loan documents and the lien was not perfected. The note references a deed of trust however no deed of trust was prepared. The business is located in a SFHA. No customer notice or increase in flood insurance coverage (property also secures another loan) was completed.

With the lien not perfected, are there FDPA issues?

Well, there is no requirement to perfect a lien for flood insurance requirements to apply (such as recording it). However, in this case, it sounds like there is no lien to perfect in the first place.

If unsecured, flood doesn't apply.