I did a little searching, and “genanki” has been the cause of similar issues before. Someone should probably make sure the maintainer knows about this.
As far as updating the deck – you’re right that once a user has imported the deck, their own New-queue positions are what control. You can’t overwrite those with another import. You’ll have to include instructions for how to Reposition the cards correctly or use suspend/unsuspend to make sure the cards are introduced in the right order.
For your own collection – there are risks when you have the “shared” version of your deck also be the “study” version of your deck. Since you can only use Reposition on New cards, you may need to find a way to de-couple them. And you’ll have to be careful to make sure that the shared version continues to be update-able. [These are ideas that I haven’t experimented with, so please test them first, and use backups to protect your data.]
That could be –
- Temporary – export your study deck to preserve your own progress, reset the shared deck to New so you can use Reposition, reshare the deck, and then import your own progress to re-update the deck.
- Permanent –
- For your study deck: export your study deck, import that into another profile so you can make it incompatible with updating and then import it into your main profile as a separate deck.
- [Another option is to use your existing profile and AnkiWeb account for sharing, but create a 2nd profile and AnkiWeb account for your personal studying and import your entire collection there.]
- For the shared deck: reset the deck to New so you can use Reposition, and reshare the deck.
- For your study deck: export your study deck, import that into another profile so you can make it incompatible with updating and then import it into your main profile as a separate deck.