Removing the ILV info with PgcEdit should not affect the way the standard main movie is played.
However, if the beginning of the remaining cells are made of open GOPs, and you remove the extra cells with VobBlanker, they are now beginning with broken GOPs, and that can cause the glitches on the first frames. To avoid that, it is necessary to re-encode the first I frame of the cell, to close the GOP properly. Obviously, it's not easy to do for VobBlanker, as it has no encoder, but, according to
another thread, I think jsoto is working on that problem.