Two things to consider:
- once Shady Accomplice is placed and its effect is resolved, it doesn't matter where it is in the fort, moving it up or down a floor doesn't (typically) affect your score
- many persistent cards give you better effects the higher up the fort they are
As an example, say I played Harbinger's Mask on the ground floor, hoping to play another persistent effect card on that floor to score points. But for whatever reason I didn't manage to do this. Playing Shady Accomplice on the middle or top floor let's me reposition Harbinger's Mask to potentially score points. Obviously, getting it into the top floor is the most ideal situation because then its effect applies to the whole fort.
The card is sort of like a second chance.