Hi Izzy

One option is to grant an extension to those users who have submissions pending so their existing submission doesn't disappear 

You can then restrict access to the second assignment based on non completion of the first assignment. The activity completion conditions of the first assignment would be viewing or maybe submission of the activity 

If you want to have course completion tracked then this could be based on a course total rather than completion of activities because activity completion is based on viewing the activity.

Let us know if there are any issues with this.

Regards