Several months ago I worked over my site .htaccess file to eliminate the possibility of returning a 200 response for malformed urls. If a page doesn't exist a 404 response is the result, the site no longer makes a best guess redirect. Over the years this site had picked up countless links containing malformed urls, it was due for a cleanup.
As expected the number of 404 errors reported in GWT shot up and I diligently went through the list regularly and cleared it. After a couple of months of doing this daily, on March 15th to be specific, I stopped logging into GWT. Monitoring these 404 errors in GWT had become a chore without benefit. On March 23rd I received a 404 error email warning and every day since the crawl rate has been 3x normal.
All of the previously cleared 404 errors are back. My concern is that when I was clearing the errors the crawl rate was normal but now that I'm not it's 3 times higher than normal. Should I go back to GWT and clear the errors when 404 is the right response? I'm inclined to let Google get a good dose of the 404's and, eventually, stop crawling them as they weren't intended to exist in the first place.
Clearing 404 errors in GWT can seemingly return the crawl rate to normal, but is it a good idea? Traffic, and rankings, remain unchanged.