In business, I would use such lower case letters to indicate the initials of the person who actually drafted the letter, as opposed to the person who signed it.
You may have a series of lower case letters, representing those who concurred with the content of the letter (e.g. the drafter's supervisor or the appropriate "subject matter expert") The capital letters may refer to the Department concerned or the filing location (the latter particularly if accompanied by numbers)
Hope this helps
PS If you saw the letters cc: jbl/nt/bd at the end of the letter, that would mean that the people represented by the initials would receive a copy (cc standing for "carbon copy - as typewriter copies were originally generated via "carbon paper"). If the originator's copy also had "bcc:den" that would mean that the person with initials "den" should get a "blind" copy, i.e. the other recipients would not be aware that "den" had been copied on the letter.