I haven't looked into the actual code fix, but given the "reset" name I have to think it has to do with SQLite "thinking" it has copied more pages than it actually did.

i.e. The checkpoint starts, and a write hits after the modifications to data structures have been done but before the data has actually been put in the database. The process starts over again, but doesn't undo the changes it made to indexes etc. Hence the db thinks it holds pages that don't exist.

That's my interpretation, anyways.

My interpretation is that they haven't been copied because they didn't exist?

If you have 10 pages and it tries to copy 20, either those 10 pages wouldn't really be copied, or bogus data would be written.

That's how I read at least. Those things are not mutually exclusive.