Probably as a by-product of "The Burn."
Possible, but unlikely.
In the case of 20th century files being somewhat fragmentary in the 23rd century for example, Earth went through various conflicts and wars (most notably WWIII which was the biggest conflict).
WWIII likely may have damaged some records as redundancy wouldn't at all be as widespread on a planetary level at that time (aka, different nations not working together).
However, when the Federation was founded, data redundancy would be ridiculously huge.
You wouldn't be storing this info on 1 planet (such as Earth)... data would be stored in databases across the Federation...
A single starship can easily contain the ENTIRE Federation database... that's practically all collective knowledge of ALL UFP species in a single computer core onboard 1 ship.
Stalfeet had 7000 ships in active service by the 23rd century... this number was likely bigger by the 24th century and so on and so on.
Then you have member species planets which would ALL have copies of Federation database across a planet in multiple locations... (over 150 different Alien species are part of the Federation by the late 24th century).
Then you have to factor in colonies in existing star systems (SOL, Tellar, Vulcan, Andoria) on asteroids, moons and planets.
Different colonies throughout Federation space...
Its unlikely that everyone would be constantly connecting to a central database across large distances.
Sure, we've seen that there is such a thing as 'central archives' on Qo'nos in the mid-late 24th century... but we're talking about stuff from the 32 century.
Admittedly, we don't know exactly what 'The Burn' is/was, however, I find it unlikely that even major wars throughout UFP history (such as the Dominion War) would cause data fragmentation because it didn't really affect large number of planetary bodies or colonies... in fact, the data lost would be from starships that were lost in battle... but on a large scale, this is minor, and all of the data pertaining to the war, or files BEFORE the war or immediately after it were left intact.
For Starfleet that has backups for backups in the 24th century, it would be kinda surprising (ludicrous even) that 0 data on Discovery exists by the 32nd century... or that data about the 23rd century is fragmentary by that point.