If you check the box for "Apply to method code", it won't change the font for windows that were already modified with another font.
I usually do one of the following -

SET RESO OFF
USE (SYS(2005)) EXCL
** change from Courier New to something else.
DELETE FOR "courier new" $ LOWER(data)
** or
** changing to "Verdana"
DELETE FOR LEFT(id,4)="WIND" AND !"verdana" $ LOWER(data)
PACK
USE
SET RESO ON

Of course, you'll have to right-click | Properties and Apply to.. on the first type of each window you modify, but that's better than having to do all of them.

P.S. - I tried this

** assuming resource is off and used already
REPLACE data WITH STRTRAN(data, "Courier New", "Verdana") ;
  FOR "Courier New" $ data

but it didn't seem to work. There's binary information in that field as well, so that's probably why.