You can leave, and your application generally keeps processing. The risk is coming back: you need a valid visa or eTA to re-enter, and if your old permit has expired, you would generally return as a visitor — which means you usually cannot work or study again until your new permit is approved. Also note that "flagpoling" (a quick border trip to get a permit) was ended in 2024. Many people avoid travel until the decision arrives.
Updated July 2026