Two levels, one decision
Everything your participants see lives at one of two levels. The organisation level holds your reference content, shared by every course. The course level holds the adjustments that belong to a single course. Every edit you make happens at one of these levels, so the question to ask before editing is simple: should this change reach every course, or just this one?
The two levels are connected. Each course is created from a course template and inherits the template's activities. That inheritance is what makes the organisation level so powerful: improve an activity once and every course that uses it benefits.