This is working as designed. Every time you make a change to the import config file, it's considered a new import. Since we had to add the dependency after all pages were already imported once, this changed the file hash, and they were not considered duplicates.
VaultWiki will only prevent duplicates within what it considers to be the same import. It does this to prevent data loss if you are importing from multiple sources and some of the pages have title collisions.
We can definitely improve this in the future, for example, by letting the admin name each import attempt and choose which import to continue based on these custom names, rather than just resetting when the file hash changes. That might require storing some of the config info in the database, which is something we wanted to avoid for security.