Regarding a Space Opera setting in which humanity vanished at some point, I see no reason that it couldn't work.
Regarding a Space Opera setting segueing into a Speculative Documentary, hmm... A major shift in genre can be a dangerous thing: those who were invested in the initial genre might feel disaffected at the loss of it, while those interested in the subsequent genre could miss out on it by virtue of not realising that it was coming.
(I will say that I sincerely doubt that there's one way in which everyone would react to the change; different people are likely to react in different ways!)
Still, I won't say that it's impossible to pull off, so I will step aside on this point for now, to let someone else give further comment!
Regarding human colonies, that depends heavily on the specifics: On whether there were non-humans in said colonies; if so, then on how feasible it is for the non-humans to take up the duties of the humans; on what automation, if any, is present; and more besides, I daresay.
Of course, a colony that had only humans would arguably cease to be a colony, as it would lack inhabitants.
My Games & Writing
What would you think about Space Opera setting that all human mysteriously disappeared? since I have this concept based on idea that what if we transplant Life After People premise to Space Opera genre such as Star Wars,Star Trek,Gundan,Warhammer 40K etc? How would everyone have think about Space Opera setting that suddenly turn into Speculative Documentary after all human disappeared? how would various humans colonies around the galactic sphere survived without human to sustain the world