These changes are described in OpenTreeOfLife/phylesystem-api#191. For useful behavior for interpreting the old properties, see this code in the curation app that tries to modify incoming Nexson using information known to the client. (N.B. this code uses the wrong property name and values, should be tree['^ot:candidateForSynthesis'] instead of tree['^ot:readyForSynthesis'])
A server-side process can probably do a better job by detecting which trees are already in collections that contribute to synthesis, and therefore should have their ot:candidateForSynthesis property set to ot:include.