Did you print your Family Journal to a file? End notes are not available when printing to a file. And, depending upon your choise of footnote options, the source can be cited in full, abbreviated OR if you have chosen embedded notes for a family journal format, the source citations are included in the body of the report with Individual Records Footnotes and Event Footnotes printing as the end notes.
You might also want to run the Utilities/Program/Check/Repair feature, as the Source Links may not be associated in the source librar. If an associated source is not found, the source is restored to the Source library when the Repair option is chosen.
These are the only things I can think of at the moment. Perhaps someone else has ideas for you.