The better enders are 1,2 and d4. Test if those work.
Okay, just tested a bunch of stuff out.
The hitbox for the specific sequence [f4, up missile] has totally changed from pre-patch, and f4, up missile is now very different from any other move before an up missile.
[f4, up missile] and [TU, f4, up missile] goes through the opponent. Even worse, after this sequence, the first hit of any rush down after (like the b3 of a b3,4 starter) will also go through the opponent. What's weird is [EX TU, f4, up missile] still works right.
But, out of about 50 tries, I DID get the up missile to connect 3 times in this [TU, f4, up missile] sequence. It is very hard, but you have to do the f4 as late as possible after the TU, then the up missile as fast as you can. This isn't practical or reliable, so scratch doing that sequence. The reason it works very late is for some reason there's a short time window where the opponent is invisible after the sequence, and doing it late passes the time.
Very weird that these still do work:
[TU, f4, up missile] and [f4, up missile] do NOT work.
[EX TU, f4, standard up missile] does work.
[TU, f4, far up missile] does work when opponent is rolling back.
[TU, f4, close up missile] is almost impossible for me to test, because the negative edge instantly does a TU for me.
[TU, f4, homing missile] does work because it hits later than a regular up missile.
[TU, f4, straight missile/EX straight missile/flame/EX flame] all work normally as a combo.
[TU, b2, standard up missile] does work, and also any quick rushdown after it.
[TU, b2, far up missile] does work when opponent is rolling back.
[TU, b2, close up missile] also hits opponent when they do rushdown.
[TU, b2, f2/ TU, b2, f2+BL] (2 in 1 flame/2 in 1 EX flame) still work normally.
[TU, b2, f1/ TU, b2, f1+ BL] (2 in 1 missile/2 in 1 EX missile) still work normally (timing is still strict).
[EX TU, b2, and all above] all work normally.
All [TU,1,2, up missile] and [TU, d4, up missile] sequences work just like the b2 sequences above - the same as before.
The only sequence that has changed to my knowledge is the f4, up missile sequence.
I have tried the [f4, up missile] sequence as human Sektor, and MK3 Sektor. I have tried it against about 12 different characters of various heights and DLC. It does not work for ANYONE.
So in summary:
The up missile in a [f4, up missile] setup and any subsequent rushdown hit will go through your opponent. This has been changed from prepatch, and Sektor's other up-missile setups still work normally. The reason is that specifically after a [f4, up missile], there is a short window that the opponent is invisible/invincible that isn't there on any similar setup. F4 was probably his best up missile setup starter after a combo, and taking it away sucks. This is either a glitch or an intentional nerf.