My question now is, how thoroughly does one of the Yuris have to be destroyed in order to prevent the universe from collapsing? Is erasure-by-gnosia the only acceptable method, or would it be sufficient, say, for bug-Yuri to throw themself into a sun before real-Yuri wakes from the healing pod?

This kind of twist is exactly what I stayed for. It’s the classic trope where the protagonist is revealed to be the clone / ghost / villain, but it hits hard every time.

There’s one hack for the universe to continue existing even without Gnosia infectees: our Yuri (a.k.a bug Yuri) just have to get rid of the real one and take their place. (Maybe that’s why doppelgangers are always so obsessed with taking the original’s place in fiction…)

Edit: Here’s my theory:

the Gnosia infection originated from Liu An, and would have been contained there, never spreading further. Even the ship they are on would see the humans defeating any Gnosia onboard in some in-universe canonical timeline.

Gnos sees all these, and so sent its agent, bug Yuri, Terminator-style to this ship to ensure the propagation of Gnosia. It would actually want the universe to end when there are no Gnosia onboard.