One of the EPA's three reasons

Rodents and Insects in the Ducts

An infestation is one of the three situations in which the EPA says to consider duct cleaning. It is also the one where cleaning done in the wrong order is wasted.

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The order matters

Seal, Then Clean, Then Repair

Close the way in. A pest control company finds and seals the entry points and deals with what is still alive. Cleaning before this is done will need doing again.
Clean what was left behind. Droppings, nesting material and debris are removed from the affected runs, the trunk and the return.
Repair the ductwork. A duct with a hole chewed in it leaks conditioned air and pulls in attic air. Replacing that run is a licensed air conditioning contractor's work.

The three steps may involve three different companies. A single quote that claims to cover all of them deserves a careful read.

What to look and listen for

Signs Something Is in the System

Scratching or movement overhead, most often at night.
Droppings on the attic decking near the air handler, or visible inside a register.
A smell that arrives when the fan starts and fades when it stops.
Shredded insulation, or a silver duct jacket with a ragged hole in it.
Insects appearing at one particular vent.

Flexible duct is soft enough to chew through, and an attic is warm, dry and rarely visited. Leave droppings and nests where they are for the crew.

Scope

What the Cleaning Should Reach

The return duct and the area around the air handler matter as much as the supply runs, because that is where air is drawn in. A full job covers both sides. Ask for photographs of the worst of it before and after, and ask which runs, if any, the contractor thinks should be replaced.

After an Infestation

Is duct cleaning enough after rodents?

No. Cleaning removes what they left. If the way in is still open they come back, and if they chewed through a duct that run needs repair.

Can the ducts be disinfected afterward?

In Texas, applying a disinfectant inside the system is work for a licensed air conditioning contractor, and the EPA notes that no chemical biocides are currently registered for use in internally insulated duct systems. Ask exactly what product is proposed and what it is registered for.

Should I keep running the air conditioning?

If you can see droppings or nesting at a register, or there is a strong smell when the fan starts, it is reasonable to leave the system off until someone has looked.

Something in the Attic?

Say what you have heard, seen or smelled, and whether pest control has already been out.

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