The excess water in the canner changes the volume of air, the pressure and the temperature achieved according to the standard guidelines. How much of an effect depends on altitude.

If less than 24 hours they should be re-processed properly. It will make them softer but they will be safe (new lids required). If more than 24 hours move them to freezer containers and freeze.

Pressure canners require 3" of water in the canner prior to inserting the jars, slightly more when the really long processing times are required.

Dave

Here is a link that might be useful: NCHFP - How to use a pressure canner