The breakpoints window is available through the Debug menu. It is a treeview with checkboxes showing you what breakpoints have been added to code in the model. You can disable breakpoints by clicking the checkbox next to the line number where they are. You can disable all the breakpoints by unchecking the "Enable Breakpoint Debugging" box. Checking and unchecking these boxes will only affect whether a breakpoint is enabled or disabled, it will not actually delete the breakpoint. To delete a breakpoint, you can highlight it in this window and press the delete key or click on its in the code window. Disabled breakpoints will appear as a in the margin and will not cause the FlexScript execution to stop for debugging.
You may right click on a breakpoint in the breakpoints window to explore the associated code.