Sometimes that happens. I try not to skip breaks, they are important part of pomodoro. But Emacs ain't my dad - if I feel like skipping a break or taking one before the end of the current cycle - I just do it. There are days when I simply can't maintain discipline of concentrating focus and taking breaks within intervals then I simply don't use org-pomodoro. I would clock-in on a task and work until I'm tired. I'm not a contractor, I don't need to report my "billable hours" yet clocking in helps me to maintain focus on the task and keep notes. There's a way in Emacs to attach a note onto currently clocked-in task without having to navigate to it.