In order to process the files marked as deleted in Clearwell, the workaround is to set case level property " esa.case.process.lef.deleted.files" to true before discovery of case folder containing LEF files. Below are the steps to set the property

Below are the steps to increase the property:

1.     Navigate to System > Support Features
2.     Choose Property Browser  From the pull down
3.     Fill out the fields appropriately
4.     Under Select the case (or system)  pull down
5.     Fill out Name of property to change enter esa.case.process.lef.deleted.files
6.     Fill out New value with the new value desired
7.     Check the Confirm change box
8.     Click the Submit button

Restart Clearwell Services for the property to take effect. Create a new case folder source in the same case and rediscover and process the L01.