If repeated courses of antibiotics don't clear it up, your vet might want to perform a transtracheal wash to see exactly what kind of bacteria are in there. That way, instead of just prescribing a general, broad-spectrum antibiotic, a more specific antibiotic can be prescribed to attack the bacteria because the "enemy" will be known instead of trying to use a drug that works on many different types of bacteria.
Some drugs, such as metronidazole (sold under the brand name "Flagyl") are excellent for intestinal bugs, such as giardia, that cause diarrhea, but for respiratory problems they're not too successful. Broad spectrum antibiotics like amoxicillin are prescribed so often that it's not all that uncommon to run into bacteria that have become resistant to them, so a transtracheal wash is extremely useful in isolating the exact bacteria that needs to be dealt with so that one of the medications that has been most successful in wiping out that particular bacteria can be prescribed.
Kennel cough CAN hang on for what seems like an endless amount of time, but after a while it gets really difficult to deal with in terms of everyone losing sleep due to the constant hacking, so if it doesn't start to respond to the amoxi fairly soon, bring up the subject of the transtracheal wash to get to the bottom of it and see what the doctor thinks.
Ghilly
Yellow or green phlegm does usually signify infection of some kind. And my first thought when you said that the antibiotics were not completely working was that she might have accidentally breathed something in and it set up an infection, like you said.. Sometimes the walls of an abscess are very tough and makes it harder for antibiotics to 'get through' If it is an abscess that's easily reached, then the usual treatment is to drain it first, and also give antibiotics. But with her abscess in this location, that's not as easy. Usually for a lung abscess, antibiotic treatment is used, and drainage only occasionally, but that does depend on what is stuck down there. A bronchoscopy might be the answer. Or continued antibiotic treatment, perhaps Metronidazole/Clindamycin? See what the vet says, but please do take her back, until a treatment is found that does the trick.
I do hope she is better soon. Please post back to let us know what happens.