From what version did you update? Are the fields (on both sides of the relationship) of type number or type text?
This may or may not be the reason for your problem, but if you go back enough versions, there was a change in the indexing that can break relationships in newly converted files when the match fields are of type text and there are punctuation type characters in the field in one table and not in the other. The addition of an extra space in one and not the other can also break the link when they still would have worked in the older version. Editing the data in the fields so that the records have exactly the same text corrects this problem.