Fix your structure, as explained below - they'll be back and
notice the file date is different and reindex it themselves.
They always manage to find new pages. If there have been
major changes, I might resubmit them all to make the deleted pages
disappear faster, but the critters have been showing up for more
than three years without my asking for them. I see robots I have
never submitted to indexing my pages.

>Also, how can I tell if a robot has indexed my site?
You can see treadmarks on your pages? If you have access to
the hit logs, look for requests for "robots.txt" -
all well-behaved robots ask for it and follow it's restrictions.