I have always read that the text at the beginning of the Imbue Spell Augment is talking about augment effects and augment effects known and that you can't replace the subclass specific augment effect with another one when you level up (as the ability to swap augments is getting errata'd in at some point, if I remember correctly). This is doubly cemented for me because the other subclass augments also share the exact same wording and the wording is not part of the augment's described effect.
Example: Bo, the Mechanist, is going from level 3 to 4, they have 3 augment effects known (Detecting, Protean, and Repellant) from Mechanist and an additional augment effect (Imbue Spell) from their subclass Spellwright that doesn't count against their augment effects known. Upon leveling up to 4, they want to learn Empowered but they don't get another augment known. So, they can replace Detecting, Protean, or Repellant. They cannot replace Imbue Spell, because "this (augment) effect can't be replaced".
Text up for debate:
"You gain the following unique effect for your Augment feature. This effect can’t be replaced and doesn’t count against the number of effects that you know, as shown in the Augment Effects Known column of the Mechanist Progression table."
I think that will be much clearer when the augments known and replacing them is properly errata'd in.
Now, this doesn't help at all with Rapid Augment and how many spell is the Spellwright meant to be able to imbue throughout a day. Hopefully we can get an errata on this soon.