In this project:
U1 is connected correctly to start with.
If I save the project, open another, then return to the test project, the VIN- pin of the custom symbol has moved off-screen indicated by the fact the net disappears off-screen.
The off-screen net can be deleted but VIN- connection point (green square) on U1 has disappeared. The only remedy is to delete U1 and add it again.
Pictures to follow.