Refine clearing and setting of debug timer

There is more fallout from the debugging added in WT-5043 and it giving a false positive. Here's a failure that should not have triggered. http://build.wiredtiger.com:8080/job/wiredtiger-test-format-stress-zseries/49481/

I suspect that the time was set a while ago and then a path did not re-initialize the value or set it to 0.