Just found this question an interesting one so I'll chime in - am used to just browsing
A similar situation just occurred during worlds where Yuzuru had the 2nd jump in his combo invalidated because his free leg touched down after his first jump. Sounds like the 2nd jump is only invalidated if they believe your weight has shifted onto your free leg - and it's an even harsher penalty in the SP due to it being an "incomplete combo".
So I'm guessing if you two-foot a loop as the second jump it should still count (probably with minus GOE) as long as your weight is clearly over your skating foot.
Skating protocol's instagram where they reference what happened explains it a lot better:
According to the rules, a skater can touchdown their free leg after the first jump in the combination, but only if there is no “weight transfer.” However, Yuzuru clearly puts weight on that foot (he goes down on his knee!) and that ends the combination. As a result, the +2T doesn’t count at all, and he receives a “+COMBO” marking for an incomplete attempt.
Adding insult to injury, according to the rules if you do an incomplete combination in the SP and receive “+COMBO,” the judges MUST give -3 as the final GOE — since you’ve violated the technical requirements of the SP. (It’s similar to how if you do a double as your solo jump, you get invalid element = 0 points.)