Are you asking whether merged contacts and companies will remain merged? If so, they will.
Alternatively, are you wondering whether this new AI-powered duplicate audit will continuously detect duplicate records, even if they have been merged before? If so, it will.
So I have merged a company with a duplicate of it.
These duplicates had different company domains attached to them.
After I have merged them, the master company record now has only that one domain set in the properties, as such I have 'lost' that other domain during the merging.
This is solved by the merge audits that is provided when you request a company record via the API because it will have a list of merge history that occured and the values that have not made it into the master record during the merging.