[eluser]OverZealous[/eluser]
[quote author="emorling" date="1252684631"]When I load an object to change a property and save it, all it's relationships are lost in the relationship table. Any idea what I'm doing wrong?[/quote]
No. The code, as you posted it, works. You must have done something different or configured something incorrectly somewhere else.
Do a little debugging, check the queries that are being run. You probably can figure it out from there.