Follow these guides:
https://wiki.ds-homebrew.com/twilightmenu/uninstalling-3ds
https://wiki.ds-homebrew.com/twilightmenu/installing-3ds
Your saves will be retained.
v27.1.0: Earth Day Release
Includes nds-bootstrap v1.5.0 (GBAtemp thread)
As Earth Day is where we celebrate a green earth, this TWiLight Menu++ release aims to also be green, with a clean-looking R4 (and maybe GBC) theme!
What's new?
Top screen of the R4 and GBC themes now uses the same font...
v1.5.0: Earth Day Release
Included in TWiLight Menu++ v27.1.0 (GBATemp thread)
What's new? (B4DS mode)
Nintendo Countdown Calendar now runs on DS & DS Lite without a Memory Expansion Pak!
Clash of Elementalists is now supported on DS & DS Lite! Memory Expansion Pak is required.
Bug fix
Fixed...
It's normal for SNES and Genesis games to not appear in TWLMenu++ on flashcards, because they don't support arguments in order to boot ROMs from other GUIs.
If Wood can though, then idk how it does it.
It sounds like the flashcard only supports running in DS mode, which means you're stuck with only using the DS-mode (WEP or Open) WiFi settings.
If you want the DSi-Enhanced games to use the 3DS WiFi settings, you'll need to install TWiLight Menu++ onto your 3DS here...
Try using either or both of said applications then.
If you're still unable to recover your save data, you may need to find another save file online, or start over.
If you're trying to use kernel/firmware to load games, did you follow the flashcard firmware steps in the TWLMenu++ flashcard install guide, and then set "Game Loader" to "Kernel"?