I have contacted Richard Ball via email, this is his reply
Generally speaking, however, the policy eGGSA is certainly to transcribe as closely as possible the original, including accented letters.
One particular accented letter that is not transcribed as such is ú - this convention was used (in Dutch) to render easily distinguishable a hand-written u from a handwritten n. Since it does not indicate any particular pronunciation or emphasis we feel it is very adequately transcribed by the letter u which, in a modern typeface, is not confusable with n - this, we feel, helps to make the text more legible to a modern reader and alters the sense or pronunciation not at all.
é should always have been transcribed, as also ç and ö where they are used by the original scribe.
S> - Dirk - with LNAB Coetze spelled Coetzë
Richard>: Yes, certainly - I think that should be transcribed as it stands:
Coetzë - also note the first entry on that page 'Radijn' the letter that looks like ÿ is intended to stand for ij and is always transcribed as ij in Dutch.
Susan> http://eggsa.org/transcriptions/stellenbosch/g7-1/G2-7-1-13.jpg Susanna Löefke
yes, although it is a bit difficult to tell if the diaresis is over the o or the e
Susan> If I have it correct: In the 2 examples I provide, if I transcribe it, I will type it exactly as stated on the image.
Richard> I would certainly do so.
I have also contact a company that specialize in this.
In a telephone conversation with Magie of TGI, her answer: If you make a transcript of a document, it must be typed exactly as it appears on the original document. I specifically asked her about the issue of the ú and ń. Her feedback was: If it is on the handwritten document, it should be typed like that in the transcription to make it a “true” transcription.(if anyone want to contact her, feel free to google the company or email me for contact details)
So all that said, I think all the funny thingetjies will stay in use. If the members of the CoGH project wish we can have a vote on the issue with the u / n.