It seems that some councils are saying that the self build exemption from the CIL only applies to new houses and not conversions.
This isn't an issue for all conversions because existing floor area can be deducted from the CIL calculation. However if you plan to add a large garage, extension or outbuilding as well then some councils (example Croyden) are trying to hit you with a CIL charge on that extra space.
If you find yourself in this position you might find this help