Dmitry,
Can't you get rid of buffering? Maybe that speeds up the process. Also you mentioned that the table is in the local disk, so, isn't it possible to open it exclusively for this update?
"The five senses obstruct or deform the apprehension of reality."
Jorge L. Borges?
"Premature optimization is the root of all evil in programming."
Donald Knuth, repeating C. A. R. Hoare
"To die for a religion is easier than to live it absolutely"
Jorge L. Borges