Reputation is lost in following cases
- Answer to a question which gets closed and ultimately deleted and a recalc occurs.
- If the answer to any question is deleted and a recalc occurs..
- If answer (question?) is flagged spam.
Regardless of the user's feelings towards the rep loss, it is always good to know what drove the reputation change, both up and down.
My request is to notify the user (may be using mail) about the reasons for reputation change whenever a recalc happens. The mail should enlist the questions and reasons for the change (not only "rep re-calc was done"), otherwise it would defeat the purpose.
This would also greatly reduce the noise about "rep lost" cry on Meta.