It is actually simple. Anything that breaks down into currency (glimmer, brightdust, shards, weapon parts, etc) breaks down one at a time. Anything that does not, goes in full stacks. Based on previous changes, it appears to be due to a limitation with the way the game engine handles currency distribution.
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Well that’s the thing, I didn’t know if the phantasmal fragments gave anything upon dismantling. I assumed so when they increased the stack size from 30 to unlimited it seems.
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So the question would be if you wanted to keep them, why delete them? If you were just testing, I would always recommend separating them to a 1 stack first.
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Separating them would be a good idea. But the only reason I would have deleted them is if they gave me something I could put to better use. If not I would continue to buy bounties with them.