Initial solution inserts lectures of selected courses into timetables and generates a starting solution, which may be good or bad, depending on the type of school and on the restrictions that are used. You will create the end solution using the optimisation tool. Initial solution never changes the possible previously inserted lessons; it adds new lessons to timetables. See Optimise and Timetables view.
Since Initial solution creates only an approximate starting solution for your timetables, you may have inserted some critical courses in Timetables view beforehand. If you have done this, you may have protected those courses by locking them with [Ctrl+U] in this window. It is also a good practice to save this solution on disk before you start Initial solution or you begin to optimise, since you can always read this file again into the application, if something unexpected happens - as it sometimes does.
The timetables are often manually and automatically created. When courses are properly selected, it is possible to assign a lot of "easy" courses automatically. It is a good practice lock those courses that are not intended to be manipulated automatically and save the file on disk before making big changes.