Can you enter Egypt on a charter flight and leave on a scheduled flight (or vice versa)?

The rule technically exists, but in practice it's not checked if your arrival and departure airport is the same (e.g. both flights through Sharm El Sheikh).

The national carrier's scheduled flights are considered more reliable — schedule may shift due to other aircraft delays, but scheduled flights get priority departure over charters.

If you enter on a scheduled/regular flight, you cannot leave on a charter flight under any circumstances or timeframe. Flight type is identified by flight number, not by the airline name.