Sometimes constraints are weak and cannot make up for large jumps in condition changes.
Sometimes references get lost in revision of underlying models or the assembly.
The best means to manage this is snapshot presets. This allows known states to be returned where the constraints are also reset rather than re-established.
Snapshots have limitations. You have to refresh them often if you are making significant changes to the components of the assembly. They can become invalid, for instance.
Another aid is to lock in the regeneration states in your mechanism constraints by providing known good regeneration values. As always, there are some limitations here as well, but it does help to know about it.