Noted bugs

No transition found: Wilderbourne Valley- Wyrmswood, Grove of Silence.

Cleric spells don't seem to be regenerating. Currently you pay mana, and then also lose the ability to cast again until you rest once more. Furthermore, when casting Magic Vestment (and I believe other spells from domains) on a test character, I found that one cast removed all memorisations, and I believe it also screwed with other domain spells on the same level.

Domain Spells - not restoring spells.

Is that a summary of the bug you found?

domains spells are being restored normaly. Are you sure that the lost of spells is not caused by using the spontaneous healing?

Positive. I haven't used spontaneous healing at all. They weren't auto restoring, and with rests I needed to reslot all domain spells to get them to memorise again.