@levelbest kindly provided details about another missing links issue in NVAlt lost all links, again - Bug Reports - Hook Productivity Forum, which I am responding to here since the titles and initial description match.
If the address of the original nvALT file matches the address of the nvALT file as you currently see it, then Hook should be able to find all the links.
If you do “Copy as Link” on the file in nvALT (as you see it now), it should match one or more entries in the database. However, the database is rather opaque to non programmers.
There is also a Hook log file in ~/Library/Application\ Support/com.cogsciapps.hook/ log.csv. This file is not currently read by Hook, but it can be examined by the user (in a text editor) to review their linking history. It’s just a text file. (It can also be imported in a spreadsheet.) If you were to search for the address of the current file, it should match a previous entry (a “log event”) in that file. If it does not, that suggests that somehow the address of the file has changed. I have not experienced this myself with nvALT (except in appearance, as noted above, with Dropbox; but in that case it is Dropbox moving files.) But it would be something to look at.