I have a selection of inner covers and bee escapes to deal with exactly this problem. For the Flow inner cover, you could use this escape from beethinking.com:
This is probably one of the best that I have:
If your inner cover has an oval hole, then you may want to try one of these bee escapes (known as a Porter escape):
I have had a lot of success with the Porter bee escapes in the past, but a lot of people don't like them. The reasons are that they get propolised shut quite quickly, and if the metal springs bend or move (which happens easily), bees can get around them. You can't use them with a round hole in the inner cover, though.
As Michael says, shaking is a good method too. In one of @JeffH's videos, you can see Jeff doing a "triple jerking down-shake" of a frame over the hive (my quotes, not his) and this is a very successful and quick method for me to remove more than 95% of the bees from a frame. It is remarkably atraumatic for the bees - they don't get annoyed and very few take to the air. They make a lot of noise for a few seconds, but then they quickly get back to work.