OK, apparently I was making this more complicated than it needed to be. I approached it differently this time. I simply loaded the VOB that needed the black screen removed into VideoReDo and cut the black out of it, then saved it as "all files" using its original file name with a vob extension (VTS_01_2.VOB) then I put it back in with its other untouched VOB files and IFO's. That worked perfectly. It plays through fine, the black screen part is gone completely and it stays in perfect sync. All the chapters are still there, though chapters after the edit, take you to a spot 4 seconds earlier in the movie than they did before, which is to be expected. I am surprised it worked; I figured the IFO's would no longer match up with the running time of the movie and something screwy would happen. Just to be on the safe side, is there anything I should edit in the IFO's to make it match up? or maybe just create new ones altogether for those VOB's in IFOEdit?

Edit: As it turned out, this played fine in PowerDVD but it wouldn't open in any transcoders (always failed when it tried to open the edited VOB) so I kicked it to the curb.