I don't work for Skywest; with that being said I think other airlines use them when they have a continuation flight.

IE Flight 5069 scheduled BOS - MIA going through ORD. Flight 5069 is BOS - ORD and flight 69A (actually 5069A but you can't do more then 4 #, so it becomes 069A, which is 69A; flight 3995 would become 995A and so forth) is ORD - MIA.

Basically, you can't (or shouldn't) have two flight plans with the same # in the system around the same depature time. This has become an issue because let's say 5069 (BOS - ORD) is delayed and another plane is used for the second segment; flight 5069 (ORD - MIA) then departs at the same time flight 5069 (BOS - ORD) is arriving in Chicago. Two planes, seperate flight plans, same company and flight #, on the same freq. Not good!!

Hope that helps.