I am assuming this is property in Mass. Otherwise, it will depend on the state. According to the information from the Secretary of State (http://www.sec.state.ma.us/rod/rodhom/Homestead_q_and_a.pdf)

 "Also, divorcing spouses are protected against the loss of homestead through termination or divorce. Neither divorce nor remarriage will affect the homestead of the spouse who still primarily resides in the home." 

Since the property never passed to the ex-wife and she is not using it for her primary residence, she does not have any homestead rights. The probate order was to preserve her homestead rights under the affidavit filed by him IF she took ownership of the property.

Homestead rights are normally only with regards to a person's primary residence.  A person can only have one primary residence. Unless the ex-wife lives at the property and calls it her primary, she does not have any homestead rights.

Any other rights and/or liens would be spelled out in the final decree.

BTW - Homestead is automatically subordinated when a mortgage is refinanced. 

"An estate of homestead shall be automatically subordinate to a mortgage on the home that is executed by all of the home’s owners. For homeowners that have previously executed a mortgage that included a waiver of the homestead protection, the new law applies to the existing homestead. This "waiver" shall be treated as a subordination and the previously recorded homestead shall be in full force and effect. As a result, there is no immediate need to file a new homestead declaration after you refinance, take out a second mortgage or a home equity loan. Although it is not necessary, it may be advisable in certain circumstances. Under the new law, you can file a new declaration without injury because the subsequent declaration shall relate back to the previous declaration."