Can a Boundary by Acquiescence apply when a new property owner disputes a property boundary after the old adjoining property owners established common boundaries that matched their respective surveys?

Possibly not, but there may be additional steps to prove prior agreement.

A boundary dispute usually only arises where the adjoining owners CANNOT find the common boundaries that match their respective surveys. Otherwise, there is no material dispute. Furthermore, some jurisdictions have strict requirements for settlement of such a dispute, such as setting out the dispute, referencing the deeds and other sources of boundaries, and setting forth the agreed boundaries, with reference to a new certified survey, and recording a jointly signed document in the registry of deeds.