Personally-- as a new light who's never masterworked anything-- I'm ONLY going to masterwork exotic armor. I don't have the time or resources to masterwork stuff that I'm going to bin in a few months! I'd suggest keeping the masterworked armor, though, just in case bungie reverses sunsetting.
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Yes you could keep it, but while you don't get Ascendant Shards back you do get a fair amount of other good materials like Enhancement Cores and Prisms that go a long way to generating a fresh Ascendant Shard. So it's something to consider.