I keep stumbling over the following citation/indexing format for letters from Ambrose of Milan:
epist. 49[59],3
How can I understand which letter is meant by this numbering scheme and what do the other numbers mean?
Where are you reading this? I'd check the front/back matter of the book to see if there's a reference to which editions they're referring to.
Failing that I'd grab thr Fathers of the Church translation vol 26, and look through the front material again.
Usually this kind of dual numbering is because of something like 2 standard editions.
The first number would be the letter number, the bracketed number an alternate numbering of the letter, and then the final number here would be a chapter/subsection within the letter.