So my situation is that I gained PR in May 2015 and left February 2017 a couple holidays in that. I’m planning on going back in September. Will they have an issue with that being that my 5 years is May 2020 since I was out of the country since 2017?
You shouldn't. You have approximately 600 days of presence already (maybe more), and you need to show that you will have 730 days of presence by May 2020. That is easily doable from Sep 2019-May 2020, so you will not have an issue.