IFR departure from CLT questioned ATC's apparent confusion regarding routing and ATC's comments regarding the timing out of their flight plan.

Narrative

We were given take off clearance on Runway 36R; Hornet 6 Meril transition SID. Take off clearance changed the altitude from 8;000 to 4;000 MSL. Through 2;000 FT contacted Departure and were given heading of 090. The Controller then said direct Meril. Then the Controller ask if were RNAV capable. We replied we were. The Controller changed our SID from Hornet 6 Meril transition to Meril 5 direct LILLS. I ask direct MERIL? The Supervisor Controller replied 'he gave us Meril 5 direct LILLS. You said you were capable of the RNAV. Your flight plan has timed out.' We replied we are direct LILLS. This happened at low altitude all within 3 minutes and not expecting a new SID. Confusion over the new SID; direct MERIL then direct LILLS; and our flight plan timed out. How can an aircraft be given a SID on an IFR flight plan and cleared for take off and then be told our flight plan timed out after take off? Changing SID without prior warning caused the confusion on our part which caused extra communication with the controller trying to clarify instructions.