Flan serves as the second boss of Stage 5. She will be fought immediately after the Nitori boss, just some dialogue in-between. This means that you will start this fight with the same HP and MP as whatever you finished that fight with. The boss will have 10000HP for you remove, the most of all bosses so far.
I personally used the Lost Holy Sword for this fight, as the auto attack gets over a lot of the issues with the boss being able to fly, and deals solid DPS. Every time my TIME gauge was full, I would stop time and just stand there letting the sword attack her, then when it ran out, dodge attacks in real time to quickly replenish it, then repeat.
EDIT: Thousand Daggers is your best friend. Use it.
Thousand Daggers is also a very viable option, though you will find youself lacking in MP if you use it in real-time too much (and most likely it can only be activated once per TIME stop, as it consumes 25 knives). You can just pop in and out of stopped time, just spamming the skill. This method will be probably be faster than the one with the Holy Sword (it is the strategy for the Boss Rush after all). It's down to preference which one you want to use