Will F1 visa out of status cause problem on return?

I was supposed to graduate in fall 2016, but my gpa fell below 3.0 because of medical reasons. I failed to notify in timely manner. Later I applied for re-reinstatement. Something strange happened then and I was informed that A manual entry had cancelled my request and a decision wasn’t made yet.

Later, I applied for leave of absence for a semester and canceled my request. Also I successfully applied for retroactive withdrawal from last two semesters. I will be getting a new I-20 when I resume education.

My question is, will it cause any issues on my return? Have I accrued out of status days as the decision was still not made on re-reinstatement? Can/should I apply for a new F-1 visa?