I'll briefly explain the process of changing all pokemon from a savefile to a specified trainer.

0.- Connect to My Pokemon Ranch with your DS trainer and deposit a pokemon. If the ranch is full see side notes*
1.- Use Savegame Manager Gx to extract your savegame (extract, not copy).
2.- Put savedata.bin in the same folder as the PR tools.
3.- Run PR-extractor.exe. Sort by number.
4.- Get the .tnr file of the LAST pokemon extracted. This file contains the hex data from your trainer (TID, SID and Name).

5.- Drag and drop your .tnr file to "Insert_tnr_and_update_hash.bat". The file "savedata_hashed.bin" will be created. The program will ask you if the trainer had connected to the ranch, select YES if the new trainer information matches any of the ranch trainers.

6.- Delete savedata.bin inside the folder you extracted with Savegame Manager Gx (0001000157424d50 for PAL savefile, 0001000157424d45 for NTSC-U savefile).
7.- Copy savedata_hashed.bin to that folder and rename it as savedata.bin.

8.- Restore your savegame to your wii with Savegame Manager Gx.

9.- You should now be able to extract all the pokemon with the specified trainer

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Side notes:

*: if the ranch is full, backup the savefile, then erase it and start a new game in my pokemon ranch, deposit a pokemon and extract this new savefile (in another location, don't overwrite the save with the pokemon you want to obtan!). The use this savefile to obtain your .tnr file. If you do that, select NO in step 5.

If you want to change the savegame's region/language, drag and drop savedata_hashed.bin on PR-regionchange.exe after step 5 and use the new created file instead in further steps.