My advice is to record your simulations at the size you need in the first place. I know this isn't what you want to hear but you'll get better results. I also try to avoid FMR as well. For example use page down rather than scrolling.
I have a same issue. I recorded the simulations with 600px height but client wants more blank space in height to add CC, copyright text, and other information. So I rescale the project from 600px to 630px, because If I select 630px height in the initial stage, the recording screens acquire the complete slide edge to edge and then I don't have enough space to add these information.
And rescaling the project disturbs the FMR slides.
As I've indicated, resizing projects with FMR can be problematic. I've never had success in resizing simulations. I do also try to replace an FMR with static screenshots instead of full-motion simulations. They're just easier to work with under the circumstances you describe. Remember this is just a user forum. If you are unsatisfied with my answer I suggest you reach out to support at Adobe and perhaps they have a workaround for this situation.