Hmm. I don’t think it’s recommended to require a specific font for a translation these days. It sounds like it might even be a pre-unicode or only semi-unicode font if it is using a code-point for dieresis (2 dots) and showing it as a tilde.
I would therefore encourage you to make the underlying text of the whole project into true unicode. Probably there are people here or on the Paratext site who can help you do that.
But, let us assume that for aesthetic reasons you need to use a specific font, which is using the wrong glyphs for certain letters.
Enabling full menus, you will see the advanced tab, you will see a checkbox you should set, ‘Apply changes.txt’:
In that file (click on edit), you can apply regular changes, one per line, and also restrict the change to just a single verse.
The basic format is "old" > "new"
, you can specify unicode code-points by prefixing the number with \u
For example:
"dh" > "ð"
"th" > "θ"
"\uA78C" > "\u0027"