So i figured it out thanks to everyone here and further research. This is how it works.
When you play any game i.e. Golden Sun, and save, the save is not written to the SAV in your microSD at all but sent to the SRAM. Only when you boot up the game again, it will grab the SAV from the SRAM and finally write it to your SAV file in your microSD.
Knowing this, i did the following:
Run any other GBA game in your cycloDS and save.
Modify SAV on PC, and transfer modified SAV to cycloDS.
1) Open any GBA game on your cycloDS other than the one you want to swap from VBA to CycloDS. In my example, i wanted to swap Golden Sun saves, so i will open the game Mario and Luigi Super Star Saga.
2) Save the game, so now the Mario and Luigi game save is now in the SRAM and not Golden Sun anymore. (That is the important part). Turn off DS.
3) I grabbed my Golden Sun.sav from my microSD, and put it in the BATTERY folder of my VBA on PC. Played my game for a couple of minutes, got some EXP and saved my game. (In VBA it is important that you do EXPORT > Battery File)
4) Now transfer the Battery file save (i.e. Golden Sun.sav) to my microSD.
5) Now boot up DS, what is happening here is your save file i.e. Golden Sun.sav is not being overwritten anymore by the SRAM save because you loaded up another game before it.
6) It should now show your saved progress from VBA.
Hi, i am new to the forum. I have a CycloDS and EZ Flash V combo, recently i was playing Golden Sun on my DS, and decided to transfer my .sav to my PC, opened it with VisualBoy Advance, played it, and passed maybe about two hours, saved my game. Later i grabbed the new .sav that was created with VisualBoy Advanced, and transferred it back to my MicroSD card, loaded my game, and now my game progress is not showing.
I can confirm playing the game on my DS, it loads the backup SRAM, then patches the game automatically, if that is a problem. I have tried this before with Mario & Luigi - SuperStar Saga, which did work after i did some stuff but i forgot what it was.
If anyone can help, i would greatly appreciate it.