The returning of lost items by patrons can be a challenge, and especially so when the item was lost in a previous ILS and has now been migrated to Koha. When migrating from another ILS to Koha with ByWater Solutions support, items that are lost prior to migration are imported with a “Migrated Lost” status. When a patron returns one of these items and it is checked in, you may notice these items are not clearing from a patron account. This is expected behavior.
During the migration, items that were marked as lost in your legacy ILS get set to a unique lost status (usually Migrated lost, LOST=7). Adding this value into the DefaultLongOverdueSkipLostStatuses system preference prevents Koha from charging the patron a second time. Additionally, the migrated lost fee and the migrated checkout are not typically linked together in Koha. If a borrower returns an item that was lost in your legacy ILS, Koha has no way to clear the replacement cost from the patron’s account because the charge and the item are not linked together.
Any items that are lost and returned in Koha will behave as expected: clearing the lost status automatically when returned and clearing any linked charges according to system preferences. Migrated lost fees do not clear because they are not linked to an item. To identify patrons who have returned migrated lost items so those charges can be cleared manually, add this report to your site:

SELECT issue_id, issues.borrowernumber, issues.itemnumber, date_due
FROM issues
JOIN borrowers ON (borrowers.borrowernumber=issues.borrowernumber)
JOIN items ON (items.itemnumber=issues.itemnumber)
WHERE items.itemlost=7