Thank you for your post.
I am unable to replicate the issue with FileMaker Pro 13.0v1 on Windows 8.
I am including a link to a potentially related post:
If you create a new file with several tables, are you able to replicate the issue?
Am I missing anything to replicate?
Hmmm, wild shot question here: Are you in Browse mode or Layout mode when you access manage | Database? Does the mode make a difference?
The mode does not make a difference, I tried it in browse, layout, and find modes and the TO still does not show up on the graph. If I go to a layout that references that TO or anywhere the TO is referenced then the TO shows up in the Relationship Graph.
I've had it happen in two different files, both hosted by FileMaker 12 server and both created prior to FileMaker 10 (can't remember exactly which version I made them with), the example I gave the image for was created in FileMaker 7 and it’s Relationship Graph is a mess, but would still hope TO’s would not go missing.
Another long shot:
Have you tried running a recover on the file?
Even if recover reports no problems found, see if there is any change visible when you open up the relationships graph in the recovered copy.
I have also had this issue. It appears it's deleting the left-most occurrence on all of that table's relationships. If I re-open the file in Filemaker 12 and save it ... the table and relationships reappear.
I have replied to your similar posting at:
In essence, I need more information about your versions of FileMaker Pro, operating systems, etc.
This issue with part of the relationship graph missing has been addressed in Filemaker Pro 14.0.1. Keep in mind there may be a noticeable delay before all of the external tables are loaded onto the graph.