Alfabet scan be adapted to write another language people probably did.
When I was trying to figure out when the Welsh people (or whatever we should call the people of Wales in Merlin's time) started writing, I came across information about the origins of the written word generally. I found that the Phoenician alphabet (basically the one we use) was adopted and altered a few times until the Romans adopted and altered it and spread it across Europe. In my second link, the author is discussing "curse tablets" were written in typical Roman script in Celtic in Britain. The author argues against the academic assumption of British illiteracy.
It should always be borne in mind that British was not a written language, and that the only language of writing was Latin; it would not occur to anyone to write in British, nor would they know how to do so ... In Roman Britain those who had enough education to know the alphabet had enough to know some Latin, and those who had none did not write at all.
(quote the author is arguing against) The author doesn't really come to a conclusion. The period the paper covers goes up to ~200. In my googling, I couldn't find anything about writing in Wales between then and about 1200-1400.
Somebody who was familiar enough with the Library of Alexandria to rescue specific books from it would likely be familiar enough with the languages those books were written in to be comfortable enough with those languages to write in them.
Another possibility is that Merlin's journals are written in Norse. Merlin is rumored to have been taught by Odin. Odin was the one to "discover" the Norse runes. If Merlin was taught by Odin, it stands to reason that Merlin's journals might be written in Norse in Norse runes.
No matter what language and script is used, Harry has a lot of resources that are likely to be able to translate them or teach Harry how to read them. If they're in Welsh language of the time, then the Welsh fairies Harry's friend's with could help. If they're in Norse, Odin could help. If they're in Latin or Greek, Bob could help him (or any number of academics). Further, there is a good chance that Bonea could help him no matter what script or language they're in.
A bigger challenge than script and language may be legibility. Ebeneezer remarks on it. Academics have high tech means of examining ancient texts. With his resources, Harry could avail himself of these techniques, or perhaps a spirit of intellect could do the same thing.
But as Morris said, if the journals become relevant to the story, Harry will be able to read them to the extent necessary for the story. For me, the only point of discussing all this is to demonstrate the plausible languages and scripts they could be in and how Harry could plausibly understand them.
