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The key issue is that ebgaramond-maths issues the following
\DeclareSymbolFont{letters} {OML} {EBGaramond-Maths} {m} {it}
This overwrites the existing letters font. This enables all of the characters which the font does provide and which are used in the OML encoding. However, it does this by telling LaTeX that whenever a maths symbol uses the letters font, it should use OML/EBGaramond-Maths/m/it. So LaTeX does this whether the symbol exists in the font or not. It cannot tell, essentially, one way or another.
To make this a bit clearer, it is helpful to look at the definition of \partial from fontmath.ltx:
\DeclareMathSymbol{\partial}{\mathord}{letters}{"40}
This tells LaTeX that \partial corresponds to the character in the relevant slot in the letters font. So before ebgaramond-maths is loaded, this symbol will be taken from whichever font is currently configured to provide letters (Computer Modern by default or whatever newtxmath is configured to use). After ebgaramond-maths is loaded, the symbol will be taken from whichever font is currently configured to provide letters. But now that font is EBGaramond-Maths which, as we know does not provide the symbol. What it provides is an empty slot - a blank.
The point of loading newtxmath is for the symbols it provides in other encodings (i.e. not OML) because these complement EBGaramond better than the defaults. Hence, ebgaramond-maths does not 'cancel out' what newtxmath does. Rather, it overrides one part of what newtxmath does.
In fact, ebgaramond-maths knocks out symbols from the default fonts, too. (You can still reproduce the problem if you comment out the line loading newtxmath.)
So the sequence is as follows:
- Default maths fonts are set up by LaTeX. (In particular,
letters is defined.)
newtxmath is loaded and overwrites large parts of the default configuration for maths fonts. (In particular, letters is redefined.)
ebgaramond-maths is loaded and overwrites a part of the previous configuration for maths fonts. (In particular, letters is redefined.)
There are alternative approaches but I think that this is the most practical and least incompatible one. Please see the question I asked about this and David Carlisle's response for the background to my decision.
[I am the package author.]
Redefining missing symbols
Note that you must do this in the PREAMBLE but AFTER loading ebgaramond-maths!
If you try to use one of the missing symbols, the package now issues an error. If you ask for help, it tells you how to define the missing symbols using the \re@DeclareMathSymbol command from newtxmath.
Here is an example of how to do this using one of the options for letters from newtxmath. Here, a new maths font, ntxletters is set up and missing symbols are defined using it. \makeatletter...\makeatother is required as the redeclaration command includes the @ symbol.
\makeatletter
\DeclareSymbolFont{ntxletters}{OML}{ntxmi}{m}{it}
\SetSymbolFont{ntxletters}{bold}{OML}{ntxmi}{b}{it}
\re@DeclareMathSymbol{\leftharpoonup}{\mathrel}{ntxletters}{"28}
\re@DeclareMathSymbol{\leftharpoondown}{\mathrel}{ntxletters}{"29}
\re@DeclareMathSymbol{\rightharpoonup}{\mathrel}{ntxletters}{"2A}
\re@DeclareMathSymbol{\rightharpoondown}{\mathrel}{ntxletters}{"2B}
\re@DeclareMathSymbol{\triangleleft}{\mathbin}{ntxletters}{"2F}
\re@DeclareMathSymbol{\triangleright}{\mathbin}{ntxletters}{"2E}
\re@DeclareMathSymbol{\partial}{\mathord}{ntxletters}{"40}
\re@DeclareMathSymbol{\flat}{\mathord}{ntxletters}{"5B}
\re@DeclareMathSymbol{\natural}{\mathord}{ntxletters}{"5C}
\re@DeclareMathSymbol{\star}{\mathbin}{ntxletters}{"3F}
\re@DeclareMathSymbol{\smile}{\mathrel}{ntxletters}{"5E}
\re@DeclareMathSymbol{\frown}{\mathrel}{ntxletters}{"5F}
\re@DeclareMathSymbol{\sharp}{\mathord}{ntxletters}{"5D}
\re@DeclareMathAccent{\vec}{\mathord}{ntxletters}{"7E}
\makeatother
newtxmathsoffers for thelettersfont. (I can't ping you from my answer as you deleted your comment there.) – cfr Dec 04 '14 at 23:13