1) The relationship isn't properly defined.
2) The indexes have been damaged and need to be rebuilt.
Assuming #2 is correct, you can go into File > Manage Database, choose the field on which the relationship is based and click "Options". Select the Storage tab, and choose "None" under Indexing. Save everything, and let FileMaker rebuild the index. See if that fixes the issue.
P. S. What you're doing is a perfectly acceptable practice.
Thanks Mike i think that did it, but gonna turn it over to my testers for review.