Skyvia import package with the delete operation uses mapping to identify records that should be deleted. For the delete operation you map only Id field. If a record with such Id is found, the found record is deleted.
Thus, you need to have records, that should be deleted in Salesforce, in your source SQL Server. In your case, the records are already deleted in SQL Server, and thus, Skyvia package can't perform delete operation for records that are already deleted in source.
As a workaround, you can create a trigger, which will copy rows that you delete to another table. The following link can be helpful for you: https://stackoverflow.com/questions/14018982/insert-deleted-values-into-a-table-before-delete-with-a-delete-trigger
Suppose, your source table is named table1, and you copy the deleted records to table2. In this case, you can create an import package with the delete operation from table2, containing the deleted records from table1. As the result, the records, deleted from table1, will be deleted from Salesforce.
Mapping for the Id field should be configured for the delete operation in the same way as for the update operation. For more information, please refer to https://skyvia.com/resources/docs/index.html?performing_update_and_delete.htm
Feel free to contact us if you have any further questions.