The first behaviour is because the CWYW was turned off and can be turned on again by just ‘format paper/bibliography’ and going to the third tab and selecting “enable”.
But the disappearing citations is strange. – you might try sending me a private message and sending me the before you did anything (you did save that - right?).
Unformating it and not having the original library available may have lost the embedded references, but then Endnote should tell you that when reformating.
Ensure you didn’t “remove fieldcodes” and just “unformat citation(s)”, or the references will disappear from the bibliography (but you said the citations disappeared).