If I don't see the X Hunters on the map can I still get Zero's parts?

Solution 1:

with only 2 bosses remaining on the map

if by this you are talking about the original 8 bosses that appear after the intro stage then yes you still have time, the X Hunters will randomly change locations every time you clear a map (may also work with escaping, have not tried), this counts cleared stages where you reach the boss room and instantly warp out

when i was playing it for the first time i only had Crystal Snail left to take out and Agile was there, a really hard fight given Magnet Mine is his weakness and with Crystal Snail being my last boss before the final stages i had to defeat him so it's possible to only have 1 boss left and have 1 X Hunter left to beat

if you beat all 8 bosses and still haven't beaten all 3 X Hunters to get all 3 Zero Parts

then in the final stage you will have to fight Zero before Sigma which is very hard, otherwise having all 3 you will face a Black Zero yet not fight him as the real Zero comes in to destroy him, saving you energy for your fight against Sigma