Homebrew PKHex + Powersaves? Is it possible?

[Ryccardo]

This method cannot, however, be used to re-encrypt/inject PKHeX-edited save files back into your game cart (although I am currently trying to figure out a way to do so via the R4i Save Dongle).

The issue is that saves are both encrypted and signed; for the longest time the keys were unknown (requiring the use of a modded console - by you or Datel's server), now that the bootroms are out (and so is a nice google doc about "3ds aes keys") it's theoretically possible to do all the dirty work on PC.
I don't know if it can already do it as-is, but 3DS-fuse is the project you should look into!

And the 3DSaveTool application provided by the R4i Save Dongle makers (which claims to be able to decrypt 3DS game saves) does not work for me

That device is from the very earliest days of the 3DS (if not earlier) and probably so is its software, which therefore may not support the "new" 6.0+ save encryption...

And no, I don't really trust homebrew firmware so any techniques requiring a hacked 3DS are out of question for me.

Your stuff, your freedom of choice; however, rejecting the most widespread and proven method only to ask for advice about another (one from a for-profit company that pumped out many shoddily-designed, short-availability products) will certainly reduce the amount of people sympathizing for your cause; man warned is three quarters saved...

 

[Temptress Cerise]

And no, I don't really trust homebrew firmware so any techniques requiring a hacked 3DS are out of question for me.

Like to add that, PowerSaves has been known to corrupt Pokemon cartridges. Had this happen to a couple of friends, back when I was super active with Pokemon.

Cyber Gadget 3DS Save Editor was so much better in the XY/ORAS days, but you needed a JPN 3DS and copy of the game.

TBH. I would just buy a cheap used 2DS, and a NTR cart for B9S, and do all save editing on that, if you insist on not having anything to do with CFW/Homebrew on your main console.