First, the limit switch triggers are due to noise. Setting the debounce in general config to 2000-5000 should get rid of the problem.
Once a limit switch triggers, there's a good chance that your XY position will be off. So I'd rehome the machine before resuming cutting.
First thing to do is jog the tool up above the work. Then scroll down in the g-code window to right before where it stopped, and use "Run from Here".