Apparently creating a post for help is like replacing something you've lost, 
only to find it immediately after replacing it.

Here's the solution to this problem:

Apparently Emacs will trick you into thinking you've changed the 
epa-gpg-program variable, but it won't actually honor that change when it runs 
a gpg call.

This: 
https://blogs.fsfe.org/jens.lechtenboerger/2017/04/12/gnu-emacs-under-qubes-os/

Supposedly I should be able to use the following to make Emacs recognize 
qubes-gpg-client-wrapper:

(customize-set-variable 'epg-gpg-program "/usr/bin/qubes-gpg-client-wrapper")

But even though I'm running 25.3.1, it didn't work. I had to fall back to a 
second option:

(require 'epg-config)
(customize-set-variable 'epg-gpg-program "/usr/bin/qubes-gpg-client-wrapper")
(push (cons 'OpenPGP (epg-config--make-gpg-configuration epg-gpg-program))
      epg--configurations)

This did the trick and actually got Emacs to recognize the changed variable.

I can now send email using emacs/mu4e and Qubes split gpg.

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