Hi yui,
The sewer boss is designed to battle of persistence. If/when you lose for the first time, the dialogue should continue and you can resume exploration of the dungeon. Running into Hydra again is then a random encounter and the damage you inflicted earlier will be kept. The last 10 HP must be defeated in 1 battle or it will heal itself up to 10 HP at the next encounter, so it does require a certain amount of battle composition/bond levels/luck. In my play testing, it usually takes around 3 times encountering it to defeat it entirely. Let me know if you still have problems with it and I'll consider redesign. Good luck and have blessed RNG!