If you have deleted the source geometry, the sketch entities will not update anymore because there is no longer a parent geometry to update!
You don't necessarily need to break the link for every projected sketch entity. As long as the source geometry the is still in the design, the reference between the 2D geometry and the 2D sketch entities can be maintained. Any healthy projected sketch entity that still has its source geometry intact can stay linked in the sketch.
Taking a closer look at this, I see that the root of the issue is not that the projected geometry has disappeared, but that a construction plane has updated in an adverse fasion.
It seems that the real issue is that the sketch has lost connection with the base plane. Please try the following solution.
1. Activate Drive Plate component (this greatly simplifies the timeline)
2. Make Construction Plane 1 visible in the Browser and workspace
2. Right click on the sketch with the warning in the timeline (sketch 5), then select Redefine Sketch Plane
3. Select Plane 1
The problem is resolved with no further timeline computation issues. I note that if I activate the top level and perform a Modify > Compute All command, all features appear to be healthy.
If I Edit Plane 1, I note that it appears to be based on the face of another component (Body:1). I suspect this component was recently edited in a way that may have caused the plane to flip or to change in someway. This forced the sketch to loose it's references.
I hope this helps. Let me know if you have any questions or would like a copy of the file.
Thanks!
Nathan Chandler
Principal Specialist