When a project is saved to a VPJ file and is later double-clicked to reload, all files should be visible in the bin (media box) exactly as they were when saved.
Be sure that the correct tab is selected - Video Files - Audio Files - or Images.
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, that choice is available by clicking the caret to the right of the Save Project button on the toolbar.
There are several trim methods. One is to trim the bin clip. Move the cursor to the start point and SET START. Drag it to the end point and SET END. Then drop it onto the timeline by dragging. Or right-clickthe clip and choose a placement from the context menu.
The bin clip remains in the bin, but retains the IN/OUT points. 
Another method is to first drop the clip onto the timeline, then trim it there. The bin clip will be unaffected - no excision.