I manged to recover a radiant from the red planet battle (no SP needed to recover).
I dumped it at my colony and then later when I was inspecting it, I realized its dmods costed 0 and were removable just like a normal hullmod.
I reloaded and tried to mostly redo my actions and the bug was not there. I arrived at my colony with one colossus (don't ask why, I was in a weird situation with fuel and supplies), and then took from storage many ships (no radiant), took crew from my colony to fulfill skeleton crew requirements and replenished CR at the dock using supplies, and went into refit. Then I went back to storage, took the radiant and went to refit again. There may be steps that I am missing but that is what I did for the most part. I removed the "hullmod" dmods before realizing it was a bug so I did not take a screenshot :/