You can either put a bee escape under the super to clear the bees out, or you can shake them off the frames back into the hive. A simpler option might be to “double newspaper” it. In other words, take the Flow super off and put a double layer of newspaper on top of the lower box. Put the weak hive box on top, making sure that you have dispatched the weak queen. Put another layer of double newspaper on top of the weak hive box, then put the Flow super on top of that. If you are using a queen excluder, put it on top of the upper brood box.
Yes, if you have shaken all the bees off the Flow frames. It will only take a couple of days for them to merge. If there are any stores in it, I would wrap it in something like a large trash bag to stop robbers from stealing them. However, you may just prefer to do the double decker newspaper I described above.