I notice that my main character Fighter/Cleric has loss all its special abilities together with the other Mage/Cleric in the group. Do these abilities get restored after you have left the asylum ? If not how to get they recovered if it at all. I thought it logical that something would be lost when you were "Drained" in Irenicus' bubble but it seems odd that the other character in the party similarly has lost her abilities. Anyone that can shed light on this topic would be greatly appreciated. Thanks.

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Once your soul is taken, you lose all of your special abilities. You'll get a new ability a bit later on, but your old special abilities are gone for good. None of your other characters should lose their special abilities. I think the exception would be if you are playing a multiplayer game where different characters were considered protagonists due to messing with the multiplayer options. In general, other than the protagonist, no one should have special abilities beyond what their class provides (set snares for thieves, etc.)

Is there any way to avoid having your soul taken? I like my special abilities .

'fraid not. Besides, most of them are no great loss. Cure Light Wounds? Slow Poison? Larloch's Minor Drain? Hah. The other three have some merit, certainly, but if you use the new ability you get properly, you'll never look back.