So I had an issue with breaking the prefab in a newer version of Unity (2019.1), where the process has changed. I found a similar issue was resolved a little further down in this forum by right-clicking on the object (Explosion Prefab) in the hierarchy and then clicking “Unpack Prefab Completely.” That should solve the problem in most cases, but not mine where the “Unpack Prefab Completely” option just simply didn’t show up. After digging around I finally found that I had to first open my Player Ship Prefab asset (right-click on Player Ship>Open Prefab Asset) where the Explosion Prefab was nested and then I was able to access the “Unpack Prefab Completely” option on the Explosion Prefab.
So Just in case anyone else finds this same problem, I hope this helps.
P.S. I believe this happened because my Explosion Prefab Consisted of 2 separate particle explosions parented together by an Empty object, and not just a single particle object prefab.