FHIR seems to be an extension of HL7 v3.x. As is the case with any other scenario where one standard is evolving from another standard, it is unclear which one to use.
Since, there is no logical way to determine which one to use, our researches must lie upstream.
From the perspective point of relevance, FHIR seems to be a more modern standard. They “aim” to be RESTFUL etc and as such, it could be expected that they have reconciled more absurdities that existed in HL v3.x; though it is unclear if the change in conceptual framework has introduced new absurdities.
Another crucial factor is the tooling around either of these protocols and their update cycles.
If any of the more respected open source health systems are leaning towards the newer version, that would be the clinching factor.