Saving the project, which creates the VPJ file, mirrors exactly what's on the timeline, the effects, transitions, etc.
If there are INS/OUTS to close, right-click between them and CLOSE GAP. If all material is on track one, use Storyboard mode for a better view of the gaps.
Save Project File AS routinely, giving it a unique # or name, so as not to overwrite prior saves. Using Save Project Files (no AS) will overwrite