This was a dsicvoery that Koha works this way, and has for some time, but goes against what we had believed happened.  This is not necessarily undesired behaviour, however, it should probably be a choice (charge/do not charge overdue fines when lost item returned if fines previously forgiven)

Filing for discussion.

To recreate:
1 - Setup:
      FinesMode: Calculate and charge (production)
      WhenLostForgiveFine: Forgive
      MarkLostItemsAsReturned: Select none
      Make sure your circ rules include fines
      Find an item with a replacement cost
2 - Backdate a checkout to a patron with the item from above
3 - Run fines.pl  - patron gets charges
4 - Mark the item lost, it is not returned, fines are forgiven, patron is charged replacement
5 - Return the item
6 - Patron gets a new fine for the overdue with the same amount that was forgiven