The inversions of an augmented triad are symmetrical, meaning the relative intervals of each inversion are the same, at least enharmonically.
C E G#
is two major thirds stacked.
But, technically, E G# C
is not two stacked major thirds. It is a major third and a diminished fourth, which enharmonically is the same as a major third.
E G# C
is not an E
augmented triad, E G# B#
is an E
augmented triad.
When you get into chord spellings and enharmonic equivalence, you should not just say it's all the same. The more obvious case is the German augmented sixth chord being enharmonically the same as a root position dominant seventh chord, but functionally the chord or very different. The former is a pre-dominant chord, while the later is a dominant chord.
We can make the same observation about augmented triads. Look at the harmonic context. If, for example, you were in the key of F
major, and the chord was C E G#
moving to an F
major triad, you would call the first chord a C
augmented triad, rooted on the dominant, a chord acting as a dominant. You don't then willy-nilly, say that chord is the same as an E
augmented triad or G#
augmented triad.
Specifically, if the we start with an E major triad and then augment the B, should we get a B♯?
Yes. An augmented triad has an augmented fifth above the root.
If you are thinking B#
is enharmonically C
, and then respell the chord to E G# C
, and then call it an E
augmented triad, instead of a C
augmented triad, you're just misspelling chords.
It isn't really clear what the "problem" is. Is it a notation issue, an analysis issue? Part of the problem is asking about "sameness." That isn't a musical term. Enharmonic equivalency is the musical term. If the question is just general, I would say: spell chords correctly, and enharmonic equivalents are not necessarily the same in the sense of harmonic function.