lm_bridge is a tool for quickly copying hacks--and other files too, I guess--to your sd2snes's sd card over usb.
This tool can definitely be used to shoot your sd2snes's SD card in its foot. In its default configuration, it should work just fine. If you do want to change the switches, read the --help carefully. And maybe use a scratch sd card. (I do!) But if not, at least back up your /sd2snes/saves directory.
I've tested this pretty thoroughly locally, and it worked when ArisenDead tested it.
-1. Have a USB enabled firmware on your sd2snes's sd card and your SNES turned on.
0. Have usb2snes.exe from this zip file running. You can try it with qusb2snes, but qusb2snes tends to have issues.
1. Unzip zip the lm_bridge zip somewhere.
2. Open LM's File->Emulator->Setup Emulator.
3. Browse to the unzipped location.
4. Select emulator.bat
5. Press Ctrl-S/Save rom in LM.
6. Press F4/File->Emulator->Run Rom.
It comes with a Windows executable, the original Python source and the batch file that I'd suggest you look at if you want to customize the switches.