init hook in WP Link will fetch the current logged in users meta value for
connections_entry_id. If found and there is a value is not empty or greater than 0 the entry with that ID is fetched from the DB and saved as a new Entry object unless when fetching that entry by ID does not return results.
When the add/edit link is display, it checks if the Entry object exists and display edit if it does or add if it does not.
So, this background, I hope helps you track down the issue.
As a thought, to manually link a WP User and an Connections Entry… Link supports the User Switching plugin or did the last time I tested. So, make sure the WP User email address and the Connections Entry have identically matching email addresses and then “switch” to that user. This will trigger the linking which just updates the two fields in the DB as noted in a previous reply before setting up the variables as mentioned above in this reply.
Hope this helps, let me know.