The spells say that they affect a creature (singular)
Invisibility says (emphasis mine):
A creature you touch becomes invisible until the spell ends.
Fly has a similar wording. It does not say "each creature you touch", or "when you spend your action to touch a creature". The spell affects a single creature. The fact that you maintain concentration on it is one of the components of the duration; the invisibility lasts "until the spell ends" and one thing that will end the spell is you losing concentration.
Fly explicitly tells you that it can affect more than one target when you upcast it (emphases mine):
You touch a willing creature. The target gains a flying speed of 60 feet for the duration...When you cast this spell using a spell slot of 4th level or higher, you can target one additional creature for each slot level above 3rd.
Invisibility has a similar wording. Your concentration on the fly spell applies to all the targets; if you lose concentration, the spell ends on all of them at once. Also, note that your selection of targets applies only "when you cast" this spell, not "for the duration". Thus, when upcast, you must select all of your targets as part of the same Cast a Spell action, on the first turn of the spell. You cannot touch one creature on your first turn and later add another creature to the spell (or as you suggest, the same creature multiple times), even if you have upcast it.
If a spell was meant to affect a succession of targets over multiple turns so long as you maintained concentration, it would be worded like the concentration spell vampiric touch (emphasis mine):
Make a melee spell attack against a creature within your reach. On a hit, the target takes 3d6 necrotic damage, and you regain hit points equal to half the amount of necrotic damage dealt. Until the spell ends, you can make the attack again on each of your turns as an action.
Can you cast the spell on two targets that are 15 feet apart, using 10 feet of movement to move between them and touching them both? That is actually its own question, and there is not site consensus on the answer - so ask your DM!