By my own admission certs are black magic to me. I'm sure someone here has done this.
If an organization aquires another organization (and all their Domain) does changing ownership and/Domain registration change the cert status?
In other words if you re-register all the new Domains to the new company will it break anything?
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Technically, no nothing happens.
However, if you have an account with a cert vendor (Digicert f ex) you may need to go through a new validation process if official records for the companies change. Depends on what type of account and what level of validation your accounts have.
If your validation expires you won't be able to issue new certs from that account, but that's it. Existing ones will work until expiry/revocation as mentioned by others.
Certs will only break in 2 situations. 1. They expire on their own 2. They are revoked by someone with access to the account.
Otherwise they will continue to work as they currently do. You can stay with your current cert vendor or any new one. You may need to verify ownership of the domain. This can be done by various methods email, dns text records, certified letter/DocuSign, etc.