Well, thanks to another thread on here I learned that the "binary" files (the apps with a long hexadecimal name but without an extension) are just QVF files in disguise.
The solution I found was to add ".qvf" to the end of each file, then import them back into Qlik Sense via the QMC. All the data & connections still seem to be there.
The only annoyance is the name of the app changes so you have to rename it after import, but it imports all its data, visualisations and connections. (It doesn't re-import the image files for the icons though - they have to be reloaded through QMC manually).