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real estate ownership transfer

You really want to have a local lawyer by hand to help you with all of this. Authorities may refuse to accept this transaction if you don't have all legal documents available to confirm this to be a true transfer / business transaction that took place!
 
I would like to keep the real estate safe and secure and no longer associated to the previous ownership.

Will the UBO remain the same? If so then don't waste your time doing this.
 
For example, UBO could be a Cyprus Ltd owned by a Belize holding Ltd. Any thoughts ?

I don't know Croatia law but if no bank account is needed for companies and land registry does not require a person as UBO then no issues. thu&¤#.

Just checkout any transfer taxes or stamp duty etc you may end up having to pay.