Kellie,
When I was going through radiation over 15 years ago, Salagen wasn't even available, but I still had a lot of nasty phlegm for awhile, so I don't think you can attribute that specifically to the Salagen. I started using it a couple of years later, during clinical trials and after it was released on the market, and have been using it steadily ever since, without any phlegm/gagging problems.
Salagen is primarily a glaucoma medicine, but one side effect is that it causes a temporary increase in salivary function (although its effectiveness varies from person to person). For people like me who do derive benefit from it, it's a really important part of maintaining some level of moisture in my mouth every day -- for eating, speaking, and overall dental health.
Cathy