Hi Ivan,
In your introductory post, I feel you've implied certain assumptions, and I'd like to suggest some alternative viewpoints. Toward the end I'll give some actual
advice, so if you get tired of my ramblings, you might want to skip to that part.

QUOTE
As things stand, you can't play a triad of E-flat (major or minor) on the left hand of a a 46-key duet concertina, either Maccann or Hayden system, except in inversion.
While "uninverted" triads are often handy, it's possible to make some fine music even without the tonic in the bass. Since you can't use what you don't have, why not learn to use what you do have before you try changing it? Experimentation can lead to some wonderful things that you might never discover if you just try to follow particular "rules" or "designs". I know it's been that way for me.
QUOTE
However the absence of an E-flat triad (except in inversion, or by picking out a note on the right hand) makes ordinary keys like B-flat major and even C minor, something of a headache to play in.
I don't believe that most of the posters on Concertina.net would consider "B-flat major and even C minor" to be "ordinary keys". What is "ordinary" depends a great deal on the repertoire you intend to play (though transposition is often an option, too). Aside from mentioning the piano and one song ("Onward Christian Soldiers"), you haven't told us what your intended repertoire might be, but apparently it's not the traditional Irish and English dance music which often dominates discussions here.
QUOTE
Now I assume "professors" Maccann and Hayden thought rather carefully about the key selection, after all they were/are good players and I am barely starting. However it does, perhaps hubristically, occur to me that a small adjustment to the key allocation would give me a more useful accompaniment instrument.
Maybe so, but it's quite possible that their intended/preferred repertoire or styles of arrangement were quite different from yours... or mine. They are not to be faulted for this. One
might fault
you for not considering the note selection and its ramifications before buying your instrument. However, I am trying to suggest some after-the-fact alternatives.
QUOTE
I have recently obtained a 46-key Maccann Duet, which I am teaching myself. As a pianist my inclination is to play chords with the left hand, and a tune on the right.
You make it sound like that's what
all piano players do. Now I'll show my own prejudice/limited experience, but I find that style much
less common among those who play in flat keys than among those who play in sharp keys. RH melody-LH chord I associate with traditions of dance music where melody is often played on flute, whistle, or fiddle and favored keys are G, D, A, and C. Flat keys I associate with "traditions" that use brass and reed instruments, such as jazz and marching bands (though I rarely see a piano in a marching band

), and they tend to have harmonies that are more complex and more evenly divided between the hands (or "hands"). Songs, of course, could be in any key, depending on the voice of the singer, but transposing by a half step either direction rarely leads to difficulties... for the singer.
QUOTE
In fact I selected this concertina precisely because with a piano background the duet seemed most likely to fit under my old fingers,...
Apparently, the correspondence -- at least with a 46-button Maccann -- wasn't quite as simple or complete as you expected. And as I think you're now discovering, there's quite a variety of different duets -- in terms of both range and keyboard design, -- and they are not all equal for your purposes/needs.
QUOTE
...you can get a decent quality Maccann for a modest investment.
Some time ago I coined a phrase: "No matter how much you paid, if you didn't get what you need, the price was too high."
QUOTE
To play every triad, major, minor or diminished, it suffices to provide a chromatic scale of 19 notes. Both Maccann and Hayden 46-key duets have 21 keys for the left hand, but the chromatic portion is only 18 notes long, in each case from E to A. It follows that precisely one triad (major and minor) is unachievable, and that is E-flat. The Maccann gives you additionally a C at the bottom and B and C at the top, whereas the Hayden gives you C and D at the bottom and B at the top. [In contrast, a 48-key Crane/Triumph has only 20 keys for the left hand, but they form a chromatic sequence from C to G, which allows one to play "Onward Christian Soldiers" in E-flat.]
True enough. In fact, on the left hand of a 48-button Crane you can play that melody in 5 of the 12 possible keys: Eb, E, F, Gb, and G. But I thought you wanted to play
melody in the
right hand. There the Crane also gives you an advantage, being able to cover those 5 keys in the right hand even on a 35-button, and
all keys on a 48. Furthermore, on the 46-button Maccann (and even 55-button Lachenal Maccanns), you would need to play that particular melody an octave higher than "normal". Also for Eb on the 46-button Hayden, though transposing up a step to F would work.
By the way, crossing an occasional note into the other hand isn't a disaster. Anglo players do it all the time, and I understand Hayden players also do it for certain notes (like that "missing" RH Eb). I do it on my Crane when the melody goes below middle C.
One thing you didn't mention is whether you intend to play your duet with other instruments. If not, you should seriously consider the possibilities of transposing. If so, you should consider using those instruments to supplement your arrangements so that nothing appears to be "missing". (You might even try doing both.)
QUOTE
How easy is it (for a professional repairer) to change...
I think Rich Morse answered that question pretty well. I would add my recommendation that if you insist on changing some notes you do so by replacing the reeds -- not altering them, -- and keep the originals. If you ever want to sell the instrument, prospective buyers may prefer an instrument without your changes.
QUOTE
What would duet players think of the following alternative substitutions?
1. Change top G# to B-flat - still has only 11 triads, but the missing one is now the less useful C# (still be available in two inversions) - and the changed key is duplicated on the right hand
2. Change bottom C to E-flat - now has all 12 triads, but lose bottom C, and on the whole I would have rather more use for a bottom D than an E-flat
3. Change top C to B-flat - now has all 12 triads, top B-flat is a useful key, but more useful with the C
I think you'll be doing yourself and your musical future an injustice if you base such decisions only on the ability to form uninverted triad chords. There are not only many other kinds of harmony (arrangements for two recorders can be fun), but there are many more chords than simple triads. (Even some of the simplest folk music and hymns use 7th chords, and your substitution 1. would lose you the upper Ab you might want for a Bb7 chord.)
Recommendations:... 1.
Don't change any notes on your current instrument for at least 6 months. Instead, explore what you can do without any changes and experiment with ways to get around what you are viewing as problems. In particular, try to replace the concept of "triad chord with tonic on the bottom" with "does that sound nice". I just tried playing "Onward Christian Soldiers" on my 48-button Crane -- in both Eb and G, -- with melody in the right hand and chords in the left. (In Eb, I even tried limiting myself to the notes of a 35-button Crane.) I discovered that several of the chords sounded
better (to me, anyway) in higher inversions, i.e., with either the 3rd or the 5th as the lowest note. At a few points in the tune I even found that I liked open intervals -- of a 5th, octave, at one point even a 7th -- in the left hand against a sequence of melody notes in the right. And don't feel you need to use all and exactly the same chords someone else did in their arrangement, or as you have played on the piano, or even the same chords/arrangement every time through the same piece.
... 2. Nevertheless, investigate the cost of making the change(s) you currently think would help you. Then check out the possibility of trading "up" to a larger Maccann, or "across" to a Crane, and see how the cost compares.
... 3. If you intend to stay with smaller duets (something which isn't independent of price), seriously consider switching to the Crane system. I have always liked the Crane system, though I've had Maccann's for longer, but that's not the basis for this recommendation. My general interest in the Maccann and also the Jeffries duet is increasing, but when it comes to the smaller duets I think the Crane is more versatile, and it especially seems better suited to the sorts of things you have in mind.
Best of luck in your endeavor, ... /Jim