Both reset options will delete all existing Duplicates Groups. The first option however preserves the "marked as duplicate" flag, as well as the master information, meaning that after the reset, the items that are already marked as duplicates will remain in their current state, and the system will know of what item they are a duplicate (the master). This information remains visible through the "item details" window: if an item is the master of some duplicates, it will show there, the same applies if an item is marked as the duplicate of something else.
After clicking "Get new duplicates" once more, new groups will be created, but items that are already marked as duplicates will not be included in any of the new groups. This will allow you to deal with the items that still need to be looked at, without having to re-do what has been done already.
In short, the first option allows you to avoid having to manually untangle overlapping groups while ensuring you won't need to re-evaluate items that you've already marked as duplicates. The drawback of this system is that in case you made a mistake, and marked as duplicate some items that are in fact unique, it will be difficult to spot the mistake (because the old groups have been deleted). Since your review is big I'm guessing that you will never want to manually look at all groups, so in your case this isn't a problem at all.
The second "reset" route is simpler: it deletes all groups, and re-instates all duplicates to their original "not a duplicate" state. This option is recommended if and only if you think you've made some big mistake and wish to start from square one.
I hope this helps,
Sergio