You must choose to learn it again but when you do it frees up a spell known slot at the level you previously knew it at.
Just a quick question. If I learn Flight as a Technomancer Spell at level 1, do I need to Learn it again at later levels spending Spell Learn slots, or can I just prepare Flight at a higher level spell slot?
There are no prepared spells in Starfinder. Both Mystics and Technomancers would be spontaneous casters if they were ported to Pathfinder.
At any rate, pixierose has it right. If it helps, think of those multi-level spells like spells you could undercast in Pathfinder. If you know the level 2 version of flight, you can also expend a 1st-level spell slot to cast the level 1 version even though it's not on your 1st-level spells known list.