New fix release 1.6.2 focused on multiple minor data inconsistencies, and spin-off better handling.
@ShadedMemories thanks for your report, this issue should be fixed with this release. Let me know if you have more issues.
@DerBlutJager PKVault use a system of "variants", so in your case you can move your pokemon from save to storage, create a variant of your Rayquaza and use it in another save.
Consider checking "help" section on top, variants are explained in details in "storage" part.
About the mobile version it's not in current project scope, it would require way too much work & time.
No installer/updater planned, I prefer to keep the app usage basic as is PKHeX.
You should not loose any data after updating. Did you put the new exe in the same folder as the previous one ? And obviously don't forget to save your changes before exiting PKVault.