After adding a deleted lineup to my account I got this JSON response to https://json.schedulesdirect.org/20141201/lineups:
{"code":0,"serverID":"20141201.web.2","datetime":"2015-10-15T03:48:46Z","lineups":[{"lineup":"GBR-0001189-DEFAULT","name":"BSkyB - Scotland","transport":"Satellite","location":"United Kingdom","uri":"/20141201/lineups/GBR-0001189-DEFAULT"},{"lineup":"USA-NY67791-QAM","name":"DELETED LINEUP","transport":"Deleted","location":"United Kingdom","uri":"/20141201/lineups/GBR-0001189-DEFAULT","isDeleted":true},{"lineup":"USA-NY67791-X","name":"Verizon Fios Queens - Digital","transport":"Cable","location":"Fresh Meadows","uri":"/20141201/lineups/USA-NY67791-X","isDeleted":true},{"lineup":"USA-OTA-11566","name":"Local Over the Air Broadcast","transport":"Antenna","location":"11566","uri":"/20141201/lineups/USA-OTA-11566","isDeleted":true}]}
Only the 2nd lineup of the 4 is actually deleted, but the response says the last 3 are. The deleted lineup also has bogus uri and location info. Deleting it from the account fixes the "isDeleted" value on the other 2 lineups after it.