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The data is all stored server-side. The worst that could happen is the sync connection stops working and you need to redownload the files. Nothing gets deleted by these commands. They will still be on your disk and accessible by you.
If this breaks Nextcloud, it indicates something’s wrong with your installation.
I think it is generally okay to bundle the root domain certificate and the wildcard for its subdomains into a single renewal.
So for example: