If you are careful a heat gun works wonders for removing the hardened compound.

If you are serious about the task and true preservation of the old windows I would suggest also removing the glass and giving the raw wood of the glazing bed a dose of linseed oil. This will help preserve the wood and help with adhesion of the glazing compound. Unless you plan to be performing this task regularly I would also suggest that you use an oil based compound (We have had excellent results with DAP33) and not the latex crap that is commonly found today. Only drawback to the oil based stuff is that it should set for at least a week prior to painting (we generally recommend a month). If performed carefully a good glazing job will last 25 years plus. Last year I had all of our 1880's sash redone (38 windows) for the first time since I did it myself in 1974.

PS: One of my primary job functions is providing technical assistance to contractors on historic preservation projects.

Jim

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2005 C240 4matic wagon (daily driver)
87 190D - 225K (on loan)
85 190D - 312K (on loan)
2011 Subaru Legacy AWD (Wife's)