When I compile as an rtf my citations within my foot notes don’t come out as the long version. They still have their hash number fron Endnote. My citations within the bidy of the document are fine
Any ideas welcome 
Is this in regards to Endnote’s RTF scan? For a while their software was having difficulties with placeholders embedded in footnotes. I don’t know if that is still the case, but you may find some tips on how to get around that on the forums here, if it is still a problem. I know a lot of people do the code replacement in Word or OpenOffice, using the plug-in, which neatly dodges any issues with RTF scan.
I have a grudging respect for EndNote and, despite some teeth gnashing with a stray author, have it to thank for correctly referencing my doctorate. However there are two “features” of EndNote that I have had really bad experiences with: Cite While You Write and RTF scan.
My advice is: compile to Word, then create your reference list from there.