If your PrettyLinks list has disappeared, but the counts and pagination links still show at the top, then most likely your clicks table (wp_prli_clicks) has crashed and needs to be repaired. You can repair it yourself by running the following query.
REPAIR TABLE wp_prli_clicks;
If that does not work, then you may need to contact your webhost support for further help on repairing the table or restoring it from an older backup. If all else fails, then the table will need to be completely reset (losing all clicks data).