when you do the cutout, are you setting up the brood comb in a box? you should be able to get a lot of bees into the box and get the rest with the vacuum. if you are getting the brood set up and getting the queen in the box, you should have a very good chance of saving your cutout hives.
when i go, i take two deeps and 20 frames set up with rubber bands. also some 5 gallon buckets with lids. honey goes in the buckets, brood into the frames, junk comb into a rubbermaid tub with lid. when i'm done, i tape an entrance reducer over the opening and staple the boxes, bottom board, lid, etc. together and i am good to go. when i get home, the hive is basically set up and i just have to untaped it. in your case, you would then dump in your vacuumed bees.
i guess i'm not clear on how you are doing this. if you are just vacuuming up all the bees and not setting them up, i can see how you might be losing hives.
when you combine, you can spray all bees with lemongrass oil and sugar water...and/or smoke them. this masks the smell and gives them something to do. put 1 sheet of newspaper between hives, cut a couple of slits, and add box. they should do fine. give top hive an entrance by propping the lid a bit. i like to put a spacer frame between boxes with the newspaper on top of spacer, but if you don't have one, don't worry. it's a personal preference thing for me and i made a bunch of them for apiguard treatment.