Let me start off by saying, I'm probably maybe the only person with this issue lol.
I've gotten a few ships from Seasonal Events with pre-applied Transmat Effects that I didn't get specically seperatly from the Bright Engram.
Two suggestions I can think of -
* If future ships won't have pre-applied transmat effects, make collections do a one off check of what Transmat Effects are equipped on ships to resolve this issue
* Make Transmat Effects drop when dismantling ships so they get put in Collections
Would've been nice to get these ships dismantled for Bright Dust before Shadowkeep, but probably [b]very[/b] unlikely now. Only way for me to show that I have these Transmat Effects, is by keeping the ships as collections doesn't take into account transmat effects already applied to items.
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Same here, I have a ship with Cabal Drop Pod transmat effect from ages ago but don't have the transmat effect in my collection. I would love to just dismantle the ship, receive the transmat effect and reaquire the ship from collection again.