I'm not sure I understand your question, but I'll try to answer. Shield mitigation has a low base value as the concept is that you don't know what weapons will be firing at them or what angle they'll be coming from. As a target takes damage, the idea is that the crew responds by adjusting the shields and armor enhancement systems to compensate and take less damage.
After the fight is over, mitigation slowly lowers as again, you're not sure what weapons or attack vectors you'll face the next time. You seem to be asking about the logic behind shield mitigation, so I hope this provides some information. I am still confused by this:
Once that is done a small fraction of shields is lost
Your shield points when not in combat should not drop, but instead steadily recharge. My only other thought is that it's caused by an Advent ability I'm not familiar with, but that doesn't make much sense to me either. Are you sure you haven't researched a new level of shielding, thus raising the max shield points and having it look like the shields dropped in strength? If you have a replay or saved game where this is frequently occurring, I'd post it.