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Zack
When you inactivate a task, Project treats the task and all its predecessor/successor relationships as if they don’t exist.
For example, in a simple waterfall sequence of A-B-C-D-E, if I inactivated task C, project ignores task C AND the relationship between B-C and C-D. As a result, the task sequence now looks like A-B and D-E with no relationship between B-D.
Bottom line, when you deactivate a task(s), you need to make certain the proper relationships are added to cover any potential gap in the path. So in this example, you’d need to add the B-D relationship to re-establish the straight waterfall sequence.
Hope that helps