Why the on-screen checkbox alone is not enough
Gmail loads messages in pages of roughly 50, so simply clicking the header checkbox only selects what is currently rendered. The banner that appears afterward, offering to select every conversation matching the current view, is the part that actually clears a count in the thousands.
Filtering before marking read
For a specific cleanup, like "everything from newsletters" or "everything older than a year," running a search or applying a filter first, then selecting all within those results, avoids accidentally marking read messages you actually want to see.
Frequently Asked Questions
Can I mark only unread messages as read, skipping already-read ones?
Yes -- search "is:unread" first (optionally combined with a label or date range), then select all within those results before marking as read, so you are not touching messages that are already read.
Will this delete my messages?
No, marking as read only changes the read/unread status. The messages stay exactly where they are; nothing is deleted or archived.