With Pokémon Blue I have the exact same problem, actually. I tried your HxD method; it complains of the drive being full but does let you save anyway. As a sanity check, I closed and reopened the srm file on the Retrode and the new data was there (even used HxD's file compare and it said the Retrode srm had the same data as the save I was trying to copy), but as soon as the drive is ejected everything reverts back to how it was. Here's a step by step of what I've done (on Windows 7 64-bit for what that's worth):
-Confirmed RETRODE.CFG file reflects 0.18d firmware and SRAM read-only set to 0.
-Plugged in Retrode with Game Boy cartridge connected. Retrode drive contains PokemonBlue.gb, PokemonBlue.srm, and RETRODE.CFG
- Opened PokemonBlue.srm in HxD, data is visible.
- Did the copy\paste trick. Despite identical data sizes HxD issues a warning about the drive being full, but lets you continue saving.
- Closed everything, re-opened PokemonBlue.srm in a new HxD instance, confirmed it shows new data.
Is there something that should be done at this point other than ejecting the USB drive?