1. The truck will come down with less air in them.

2. The truck will come down if there is less air in them.

3. The truck will come down and less air will be in them.

4. The truck will come down, less air being in them. (*Them refers to the tires.)
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What does #1 mean? Which one is similar to #1? Would you paraphrase "less air in them'?

The antecedent for "them" needs to be in the sentence or in the previous sentence. These sentences don't read right without the antecedent.

Also ... I don't understand what "come down" means in here.

Is the truck coming down a hill?
Is the truck coming down from a bridge or overpass?
???

The truck got stuck under a bridge. The bridge was not high, so when it was passing under the bridge, it got stuck. It wouldn't move. The best way was to let the air out of the tires to lower the truck. "Them" refers to the tires.

1. "The truck will come down with less air in them" means that the truck will lower or decrease in height when there is a reduced amount of air in the tires.

2. "The truck will come down if there is less air in them" has a similar meaning to the first sentence. It states that when there is a decrease in the air pressure inside the tires, the truck's height will decrease.

To paraphrase "less air in them," you could say "reduced air volume in the tires" or "a decrease in the amount of air contained within the tires."