RYTM, Transfer, and samples, how it works?

I have projects backed up with Transfer for my RYTM MK1. I recently got it back from repairs.
When I first backed it up, all of my samples copied to my computer. When trying to put them back Transfer said they were corrupted.
I converted them back to .wav and then I could put them back.
Now when I put a project file from my computer back to RYTM, I get two pop up windows, and a check box.

The first one asks:
How do you want to organize the included samples?
_number of samples samples are included in the project.
_number of samples of them are missing on your device.

  • import only missing samples
  • import all samples

The second window shows the samples and has a check box:

  • Import samples to their original file path

I tried importing my project using all the options, and not all samples were replaced.
Are samples missing because they were corrupted and I converted them to .wav?
What exactly is happening with each pop up option?
If my samples were not corrupted would one of these options worked to back up project with samples?

Looked through a bunch of threads and didn’t find an answer.
Also read the Transfer manual and didn’t find a solution.