It seems the hashes of files aren't checked by lint, and thus files may be updated without their hashes being updated. Actually it's unclear to me why we need those hashes at all. Do they affect how wpt work? It doesn't seem to, because the hashes can be out-of-sync for long... If they don't affect anything, can we just remove them from the manifest file? I suppose that can account for a significant part of time consumption for manifest update.

They are effectively an in-band cache used to avoid updating entries that have not changed (which is really slow; if you delete the manifest and regenerate it it will take several minutes). That implies that it doesn't matter much if it's a little behind, but deleting them from the file would require adopting an alternative mechanism to avoid full manifest updates for every test change. In terms of the lint we originally linted to check these hashes were up to date and it was a disaster; it made it very difficult to land any wpt changes at all since the hashes are affected by non-test files and merges, even ones that don't update the tests present. The real solution here is bug 1473915 which is still awaiting review from a build peer :(