Have you read this knowledgebase article?
You shouldn't have to fix all the relationships and references manually. They should convert as long as the filenames and locations of the converted files are still the same as your original files.
There is a known difference with how recent versions of filemaker use text in a match field that could be an issue here.
In older versions of filemaker, "Apple", "Apple.", and "Apple*" will all match in a relationship as the punctuation type characters were ignored. The same was true for trailing spaces. In newer versions, those examples will not match and this can "break" some older database relationships until you clean up your data.
Thanks to both of you for your help, I am digesting the information.