When you face the flying bat/insect-like creature for the second time in Chapter 4-1, there is an easy way to defeat him which will allow you to still get the Soul Gem. In the southwest corner of the bottom floor, there is a small pillar of stone in the middle, with what looks to be a log with spikes coming out of it as well as a rib cage hanging from it. When Sheva tells you that it is too hard to fight and you should go upstairs, if done correctly you can just walk backwards without having to dodge around the pillar as the Boss tries to attack you. The "Dodge" button will appear, but it is not necessary. Just continue to walk backwards around the pillar and attack with whatever you have when it is vulnerable, shooting the soft portion on the back of its tail. When it dies you can collect the Soul Gem which is worth 10,000 gold when sold.