Deleted absence entries on Time Card, reappearing again.

We have absence entries for a user in the Time card for the period of 15-21 June. When deleting this row, the system allows the deletion and also successfully submits. However, when we revisit the Time Card in Administration, we see the Absence entries there again. The delete is not going through. The manual work around would be deleting these through the Absence work area, but we need to understand why this is happening for a few cases? These Time cards were created through API and have no other errors.