Hi Christina

If you delete the users from the set audience they will be unenrolled from the program and courses. 

If you want to give them an opportunity to complete the old program then only delete them when they have completed the program or you could assign these users in the dynamic audience so they are reenrolled in the program with the new program conditions.

To make sure I have your requirements right can you outline more details on what you mean by ending and relaunching the program.

regards