I am having the same issues with losing ALL links after importing enex files. Our CFO just left the company and transferred ownership of around 1000 notes to me. This is an incredible amount of knowledge that I am lucky to have, but in his system everything was linked internally to other notes in his records. After importing the notes via .enex files I get the error:
"This note link refers to a note that does not exist on this computer. Do you want to synchronize and try to retrieve it from the server?'
Once I click 'synchronize' I get an error that reads:
'The note link refers to a note that no longer exists'.
I can see the notes that the links refer to, so I know they are there.
Do you have any suggestions as to how to restore the links?
I would be forever grateful!!