Of course, make a snapshot of the timeline before making changes, but what I do is make the changes above the Secondary storyline first, to keep everything in time with the original change sheet, and then I go back and mend the timeline together and get rid of any gaps.
If the changes come from frame.io, I import the changes list (comes in as a compound clip with markers) and then I simply slice the compound clip as I go so it ripples with the timeline, and the changes stay in sync in the timeline.