I agree that flashing is very awkward and opaque. (Especially from a Mac —
it took me many hours to find and set up the right Linux distro on a bootable USB key…)
But I've just flashed my Gemini with the latest firmware,
without losing any apps/files/data, so I know it can be done!
The important points seem to be:
- You must be using exactly the same partition layout (sizes &c) as before.
- Deselect the final 'userdata' partition. (The type will change to 'Download only', which is what you want.)
The scatter file created by Planet's new online tool had some extra partitions (for Linux, judging from the names — even though I was single-booting to rooted Android!), so I edited it, comparing with the scatter file I used last time, updating the filenames but leaving the partition sizes &c the same.
When set to 'Download only', the Flash Tool will compare the partition map from the scatter file with that currently on the Gemini, and will refuse to proceed if they differ. So it's relatively safe to use.
And I guess all your apps, files, and other data is on the 'userdata' partition, so deselecting that seems to preserve everything.
Of course, it's well worth making sure you have a backup of everything, just in case something goes wrong… (It's well worth having a backup of everything
anyway! You never know what might happen.)