I'd call this a bug. You should not have to spend Ink to swap between the two and both combinations absolutely should save in the Armoury.
I also find it puzzling from a technical point of view. The concept of skills and the armory existed when they created scribing, and I'd expect it to be designed in a way that skills or skill lines can be added to the game without the need to make them "armory compatible". When they added the arcanist or new guild skill lines, the existence of the new skills alone was likely enough for the armory to pick them up and start saving them. Which makes all this feel like it's not a matter of "we haven't added armory compatibility yet" but more like "we've made active efforts to make sure this doesn't work with the armory". I could be wrong on this of course, just providing feedback on how it looks.
If you play with different Scribing combinations while using CMX, you can see that CMX isn't able to distinguish the specific combinations properly in many cases. You can get "Chilling Explosion" to do Fire or Shock damage. (Not really - the skill has been rescribed from Chilling to Fiery or Shocking - but this is how the skill appears in CMX.) So something is quite different about the way that Scribed combinations are saved - it isn't just by skillID. Each non-Scribed skill has three skillIDs: one for the base form and one for each of the morphs. But Scribed combinations seem not to have that same 1:1 relationship between skillID and combination the same way that non-Scribed skills do.
"Chilling Explosion" does frost damage, as intended.
Rescribe to Fiery Explosion but CMX still says:
"Chilling Explosion" does fire damage.
Rescribe to Shocking Explosion but CMX still says:
"Chilling Explosion" does shock damage.
If you play with different Scribing combinations while using CMX, you can see that CMX isn't able to distinguish the specific combinations properly in many cases. You can get "Chilling Explosion" to do Fire or Shock damage. (Not really - the skill has been rescribed from Chilling to Fiery or Shocking - but this is how the skill appears in CMX.) So something is quite different about the way that Scribed combinations are saved - it isn't just by skillID. Each non-Scribed skill has three skillIDs: one for the base form and one for each of the morphs. But Scribed combinations seem not to have that same 1:1 relationship between skillID and combination the same way that non-Scribed skills do.
"Chilling Explosion" does frost damage, as intended.
Rescribe to Fiery Explosion but CMX still says:
"Chilling Explosion" does fire damage.
Rescribe to Shocking Explosion but CMX still says:
"Chilling Explosion" does shock damage.
Thanks, that explains a lot! But I'm still left wondering why scribed skills don't get a unique id. I know the amount needed would be high (1 skill with 10 focus, signature and affix possibilities would need 1000 unique ids), but I'm also pretty sure they aren't using 8 or 16 bit integers to store them. Every coding decision being made always has some reason, but I also know it isn't always a good one, and at this point I'm just curious.