I'm not sure if I'm missng some part of the complexity here, but with the solution jiggawatts proposed, wouldn't the above scenario be fairly trivial to solve?
Just implement a new SKU for this special one-time (more like first time...) discount that the account manager applies to the account.
If you want to be fancy, you could code in (or leverage one of the dozen cloud tools, depending on where you're deployed) to enable the SKU for the customer at period X and remove it at period Y and replace with the previous SKU.
To ease reporting, in your main SKU table you could have a parent_sku column and a sku_type column explaining that this row is a special discount child SKU of the parent_sku. Add basic databse restrictions and validations.
Billing is complex and requires lots of domain knowledge, but IMO it's not really THAT hard from my experience.
EDIT:
IMO a harder scenario for any billing system to deal with is account manager A made a sweetheart deal to make customer B less angry, removing one SKU completely from last months bill, giving them a 25% discount for the next invoice, and giving them some freebie.
These types of requests usually end up with a lot of issues unless the business logic promised to the customer already exists.