I finally found a good cheat procedure for R4+3in1 using the save file. Example is for Ruby.
On PC:
Run an UN-patched Pokemon Ruby(U).GBA file with VBA.
(VBA/Options/Emulator/Save Type/Flash 128k)
Do many
Cheats, Save Game ( makes 128KB Pokemon Ruby(U).sav file).
On PC/MicroSD:
Copy \VBA\Battery\Pokemon Ruby(U).sav ==> R4\GBA\SAVE\POKEMON RUBY AXVE.SAV
Copy PATCHED RUBY.GBA file to R4\GBA (if it is not already there).
On R4+3in1:
Boot R4, Choose "Game", run 3in1_ExpPack_Tool.nds
Select RUBY.GBA, (Press (A) IF RUBY is not the current NOR game).
Press (Y) to Restore the save for the NOR game from the R4 save file.
Press (X) to run the Patched Ruby ROM with the Cheat-filled save file!!!
You can copy the 3in1 save to the R4, then to PC, Import Battery File into VBA, rinse, repeat.
tested - both ways!