What does it mean for a ATC to say a flight's callsign followed by "in disguise"? So I'm just a aviation fan without industrial background. 

I'm listening to Kennedy Steve's ATC communication and he said more than once like "American 600 in disguise."

What does it mean "in disguise" in this context?

Thank you.
The controller was probably referring to an airplane in a different livery but operating under the American call sign.

A likely example is US Airways. After the two companies merged, from October 2015 all flights were operated under the American call sign, but re-painting the US Airways planes took at least a couple years.

This is not standard phraseology but "Kennedy Steve" is known for trying to inject some humor into his work. See also: What does Top 1% mentioned by ATC refer to?