Steps to reproduce:
Create two elements and link them with a sequence flow. For example: a start event and a user task.
Focus on the start event and change its id in the Properties View. Repeat for the task.
Save and close the diagram file.
Re-open the file and you will see the sequence flow is not displayed in the diagram.
If you look at the XML you will see something like this:
You can see that the sequence flow is still referencing the startevent1 and manualtask1 that are the old ids.
Eclipse Kepler, OpenJDK 7