Once your application process is underway they cannot 'cancel' your application with little or no warning. According to an agent themselves, IRCC will generally give 2 or 3 attempts / time frames for submission. If you miss the first deadline, generally they'll re-issue a second one with a BFD. They contact you via email and update the online portals as you know. If you miss a deadline, it is up to you to make it known why there has been a delay to avoid any further repercussion. They won't cancel anything without making at least a second attempt with you and IRCC is obligated to hear and consider your reasoning as to why the requirements/deadlines couldn't initially be met by you; try not to worry too much. You're good!