Sum of branded and non-branded clicks is much lower than the total reported by Google Search Console


https://support.google.com/webmasters/answer/7576553?hl=en

Discrepancies between chart totals and table totals You can see
differences between the chart totals and the table totals for several
reasons:
… When filtering by page or query, the “matches” and “does
not match” totals might not add up to the unfiltered total. For
example, adding the totals for “Queries containing:mouse” and “Queries
not containing:mouse” might not equal the total values when no query
filters are applied. This is because anonymized queries are omitted,
and data is truncated due to serving limitations.”

I have the same problem. GSC reported 6,500 total klicks, 2,500 with brand-keyword, 500 without. So I am missing data for more than half my traffic. Seems like we can do nothing about that.

Also you can look at this thread here where they discuss the same problem:
https://support.google.com/webmasters/thread/4924855?hl=en