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There are a number of issues in Flex Builder that can make life difficult, some of them related to FB some related to Eclipse. You may want to look into doing ANT builds if it is really costing you this much time a day. I generally have to restart FB once or twice a day, if not for errors, then to reduce the memory from 1.5GB or more. I don't really use ANT so maybe someone that does can give you the info on how debugging works in that scenario.
Thanks for that note. There's plenty about Ant that I don't know but based on my limited knowledge of it I don't see how it would help, because my problem is not building the app, it's initiating debugging inside Eclipse.
I found a workaround of sorts for the problem: don't terminate the applications!
Previously, I would terminate the application using either the Terminate button in the Debug view or by closing the tab in the browser (Firefox). Now I just let them pile up in the browser and I rarely see this problem.
In other words, I was having lots of trouble when doing Launch-Terminate-Launch-Terminate... but now I just Launch-Launch-Launch... and clean up once in a while.