The issue appears to have been caused in editing as no sync problems were noted in your original file...
Four different scenes were isolated in the bin, then dropped to the timeline. Same when the entire clip was placed on the timeline, then scenes were excised. Perfect sync on all.
Method one: Right-click the clip in the bin and COPY. Then in a blank area of the bin, press <ctrl-V> to paste. Repeat for as many clips as you intend to use. Each will have an incremented number and can be renamed.
Leave the master clip as is. Select clip (1). Under the preview window move the red cursor to the start point of the desired scene. Click the Set Start button. Move the cursor to the end of the scene. Click Set End. Trim other numbered clips for different scenes in the same manner.
Then drop those clips to the timeline in the desired order. Or select each in turn and use the Add button. Click the button's caret to see a drop-down placement menu. 
Method two: Place the master clip on the timeline. Split out and right-click|delete unwanted clips. Drag the clips that remain to the bin, one-by-one, where they will become individually numbered, as in method 1. Then they can be dropped back onto the timeline in the desired order.
If you make a mistake, press <ctrl-z> to backtrack, step-by-step. Always 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. From the HOME tab, the AS choice is available by clicking the caret to the right of the Save Project button on the toolbar. That way you're protected, and shouldn't lose anything.