From the name itself, system updates referred to improvements that happened to the system, such as making certain features of the system more efficient, or adding more features that would help the user of that system do other tasks more efficiently.
Of course, the author of the book Valyr was reading quickly clarified that the term 'system updates' did not catch on at first amongst the humans, instead referring the phenomenon under multiple terms related to the word blessing, awakening, ascension, and so on. Though the author of the book later went on to mention that even though that was the case in the past, the humans still recorded the differences between each system update, which Valyr was surprisingly able to read through this book.
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