It makes sense that all the mainstat stims turned into mastery stims in 4.0. There's a direct 1-1 correspondence from old mainstat to new mastery. Okay.
But fortitude stims were different, they gave the users Endurance + Defense Rating (vs. Main Stat + Power).
I realize it was probably just a search and replace oversight, when converting the mainstat stims, and it's probably too late to fix the issue since the stims are now converted to Mastery. But to correct it, you could establish a temporary vendor on fleet that would sell Fortitude stims and accept as payment Mastery stims of the same item level.
I can't speak to the full extent of the item levels or rarities affected, but I can tell you that (at least) the:
-- Prototype Anodyne Fortitude Stim (Blue)
-- Advanced Anodyne Fortitude Stim (Purple)
were erroneously converted.