You may see that lines appear in your timetable list on the app and website even though they aren't currently running in the published and current dataset. This is because Line information is stored separately in Passenger Cloud to a Network Dataset and is saved permanently. So, if the line is running in future datasets the information for that line isn't required to be uploaded from scratch to Passenger Cloud.
You can, however, import a network update including new and removed services, and manage which lines appear in the app and on the website at any given time, regardless of the operating period of the network dataset.
Simply navigate to 'Network' > 'Manage Lines' in Passenger Cloud, and select the line you want to edit. From here you'll be able to set start and end dates for when the line should be available to users in the apps and on the website.
If this information is set incorrectly, lines can be shown with no timetables. Updating the end date to reflect the date in the past that the Line finished running will remove the Line.