I know that you sort of solved this, but what did you mean with “the whole thing rewritten again to disc”? the whole database, table, record?
With a database, one record is normally the smallest item being saved, but depending on the underlying disk driver and also hardware the real saved data can be similar in size or much larger. SSD for example rewrites a whole hardware block that could be around 4k of data that could belong to different files. 🙂