Breakpoints are respected but the code is around 700 lines long and I don't want to have to set a breakpoint manually for each line everytime I restart matlab.
Why do you need to set a breakpoint manually for each line? I would set a breakpoint on the first line then step through the code from there.
If you need to restore the breakpoints, call dbstatus to create a struct array with information about the location of the breakpoints and pass that struct array into dbstop to restore those breakpoints.
If somewhere in the "black box" code you're running or in your code, if you're calling clear all then that would clear the debugging state. Try removing that and see if the error breakpoints functionality does what you need.
