How can I bypass this fontconfig warning to edit grub successfully?

Githlar's answer removes the warning, without responding to what the warning is telling you. It's actually saying that loading from ~/.fonts.conf will be removed in the future. Hence, Githlar's solution will ignore what will break in the future. The correct thing to do is to move ~/.fonts.conf to ~/.config/fontconfig/fonts.conf . The easiest way to move this (hidden) file is using the terminal and doing

mkdir -p ~/.config/fontconfig/
mv -i ~/.fonts.conf ~/.config/fontconfig/fonts.conf

There is actually a bug report filed against the vagueness of this warning.

To get rid of this message, edit the /etc/fonts/conf.d/50-user.conf file as root:

sudo nano /etc/fonts/conf.d/50-user.conf

or

sudo gedit /etc/fonts/conf.d/50-user.conf

Look for the line that says

<include ignore_missing="yes" deprecated="yes">~/.fonts.conf</include>

and change it to

<!-- <include ignore_missing="yes" deprecated="yes">~/.fonts.conf</include> -->

Doing so comments out the line. Notice that's its under a comment that says "The following elements will be removed in the future." Therefore, commenting out this line should not hurt anything.