If you happened to swallow a fly or swallowed fly eggs then the flies or fly eggs would quickly be killed and dissolved by the stomach acid.
Your stomach acid is powerful enough to where the fly eggs or flies could not survive for very long before they died as a result of the stomach acid.
I've swallowed flies on accident before several times and never have I gotten sick and the stomach acid would dissolve the flies and fly eggs before they caused any health issues.
The worse that would happen is you get vomiting, diarrhea etc as a result of the fly eggs or flies in your stomach.
But other than that you will be very safe and okay if you happened to swallow a fly or fly eggs.