Moving objects after using the Alignment feature could make the Alignment dot indicators seem to disappear. This happens whenever you have two or more objects which are selected and exactly on top of each other: overlapping handles are invisible.
The relationship between the objects still exists but the dot indicators are on top of each other and canceling each other out.
Try this test to recreate the problem:
1. Create a square of any size.
2. Duplicate that square.
3. Select both squares.
4. Choose Alignment from the Arrange menu.
5. Check on the Create checkbox.
6. Click on the Align Top button (top row, first choice).
Notice that the relationship is indicated by a dot on each square.
7. Move one square on top of the other.
Note that the relationship dots has disappeared.