Hey there. For a Y1 shader like that, it had to be in your inventory as an unattached shader during Season 3 at the earliest, which is when collections tracking went live. Shaders earned during S1 or S2 that had been applied to items, like gear, or ships, did not count for this, and did not get added to Collections. Because that shader was not unlocked in your Collections, switching your ship to something else effectively made that option disappear, without deleting or dismantling, as you said. That part is unfortunate but also expected, only shaders in Collections will be available for it.