A lingering musty smell is an indication that moisture, fungal growth and or decomposition providing the source of the odor are present. You don’t say how extensive the flood was, nor mention the source or contamination level of the water, which is a determining factor in how the clean up should be approached. Carpet cushion is difficult to dry and or decontaminate under a carpet and would be suspect. So are damp drywall, particleboard and structural wood in walls and floors. Look for anything not completely dried out and provide ventilation to speed the drying process.
If the water came from a contaminated source (Level 1 or 2) such as a sewer backup, you... — Lynn E. Krafft, ICAN/ATEX Associate Editor