@PhrozenFox No worries, we'll get to the bottom of it!
So if I understand the situation correctly:
Your main weapon is a 14 star that already has regular affixes on it that you don't want to lose
You have an S-Grade Augment (SGA) capsule that you'd like to add to your main weapon
You've checked the 2nd page of your main weapon's details and it can in fact socket your capsule's number (S1, S2, etc.)
You have a 13 star fodder weapon that can also accept your capsule's SGA
You've tried going to Monica/Dude and adding the capsule to your 13 star weapon by selecting the normal affixing option and then overwriting the affixes on your 13 star with augments from another piece of fodder that has the same number of slots as your 13 star (or more slots), but something goes wrong
Or does this step work but then you're unable to transfer the SGA from your 13 star to your 14 star (using the Transfer S-Grade Augment menu option at Monica/Dudu)?
If it's the former, I'd ask whether the capsule shows up in a message box before you select the regular augments to add to your 13 star? It should do this automatically if it detects that a capsule is in your character's inventory.
If it's the latter, I'd ask if the 13 star is greyed out/can't be selected after you choose your 14 star weapon using the Transfer SGA menu option? This shouldn't be the case if your 13 star is unlocked and has an SGA whose number can be used by your 14 star.