I am an international student in my final year of Electrical Engineering. I enrolled in an RnD course last semester and tagged it as an honor course. This is a semester-long research project where you work closely with one of the professors in your department. The work I did in the semester was satisfactory. However, it wasn't AA-worthy, so I decided to work on the project during the summer (the professor agreed). The professor I worked with is known for allotting the grades for his other courses even past the grade submission deadline. (In one of the courses, the grades were assigned two days before the course registration for the next semester began). Hence I assumed that I could work through the summer and have my grade evaluated before the start of the next semester. However, I could not get hold of him, so the grade column shows "not allotted" for this course.
So I talked about this with the professor guide at the start of this semester, had my evaluation done, and my grade submitted to the academic office within a month. However, the Dean did not approve of this, and I am looking at a potential Fail grade in this course. My current transcript still shows "not allotted".
I am applying for MS to top US grad schools. So my question is - Should I submit the current transcript with justification (in the SoP) or the updated transcript(which has the fail grade) with proper justification? The updated transcript has a slightly higher converted GPA (3.92 vs 3.9). On one hand, since I did not actually fail the course, a proper justification should suffice. On the other hand, since it's an RnD Course, it could negatively affect my chances (not sure how much, could someone shed light on this) and so "not allotted" looks better than the alternative. Also, if I do decide to submit my current transcript and get accepted, will I have problems later since the grad schools require official transcripts to be submitted after completion of undergraduate studies, and that would have the fail grade?