NM designator is listed everywhere as belonging to Manx2, not FLM or Flightline (for the record, the accident flight was operated under the NM code).
From a purely legal perspective, whoever is the rightful user of the NM code (the legal entity to whom the code was designated, based on supporting documentation at time of designation) is the contracting party for the issued tickets, irrespective of what entity collected the money. Of course if it turns out that nobody legally owns the NM code, that will raise some very akward questions...
I have checked again - from the horse's mouth, the IATA website:
Codes - Airline and Airport Codes Search
NM = FLM Aviation
Suggest you check your sources - many of the non-official decoding websites are inaccurate As Manx2 is not an airline anyway, they cannot hold a IATA code.