Posted this elsewhere, but from reading Billzard’s official announcement, it appears you do need to re-farm Cypher gear at each research level:
“You’ll be able to earn Cyphers of the First Ones currency through a variety of activities that you can use to research and unlock additional understandings to enhance your experiences in the zone. The more Cyphers you earn and spend, the higher that level will go. You’ll earn Cypher gear as you progress through the zone campaign and the occasional side quests, but you’ll also be able to collect this gear from the Cypher-Bound Chests across Zereth Mortis. When you get a new piece of Cypher gear, its item level will be determined by your current Cypher Equipment Level.”