You likely adjusted the Titles Path setting, which asks you if you want to move a few files and warns you that any existing files will be deleted. But this setting only applies to some of the loaders core files and not covers, cheats or themes.
You said that you were changing paths, so if you changed the paths for the covers, cheats and themes then the files should be in their original locations.
When you add or remove games it'll only delete cache files.
If you think you've stumbled across a bug then please send me your GXGlobal.cfg file and let me know where you've got the loaders DOL file installed. I'm assuming it's on your SD card, although normally when the loaders installed to your SD card the paths will default to your SD card.
# USB Loader GX R1281 - Main settings file
# Note: This file is automatically generated
godmode = 1
videomode = 1
videopatch = 0
videoPatchDol = 0
patchFix480p = 1
deflicker = 0
videowidth = 0
language = 10
ocarina = 0
hddinfo = 1
sinfo = 1
rumble = 1
volume = 0
sfxvolume = 80
gamesoundvolume = 80
tooltips = 1
RememberUnlock = 1
password =
GameSort = 1
LoaderIOS = 249
cios = 249
autoios = 0
keyset = 0
xflip = 2
gridRows = 1
quickboot = 0
wsprompt = 0
parentalcontrol = 4
covers_path = sd:/usbloader_gx/
covers2d_path = sd:/usbloader_gx/
coversFull_path = sd:/usbloader_gx/
theme_path = sd:/usbloader_gx/
theme =
disc_path = sd:/usbloader_gx/
language_path =
languagefiles_path = usb1:/apps/usbloadergx_r1281/language/
TxtCheatcodespath = sd:/usbloader_gx/codes/txt/
titlestxt_path = sd:/usbloader_gx/
gamesound = 0
dolpath = sd:/
ogg_path =
wiilight = 1
gameDisplay = 3
homebrewapps_path = sd:/apps/
BNRCachePath = sd:/usbloader_gx/
GameHeaderCachePath = sd:/usbloader_gx/
Cheatcodespath = sd:/usbloader_gx/codes/gct/
BcaCodepath = sd:/bca/
WipCodepath = usb1:/wip/
WDMpath = usb1:/wdm/
TitlesType = 2
CacheCheck = 1
CacheCheckCRC = 154307EB
CacheTitles = 1
patchcountrystrings = 0
screensaver = 2
musicloopmode = 0
autonetwork = 0
discart = 0
coversfull = 0
CoverAction = 0
partition = 0
marknewtitles = 0
ShowFreeSpace = 1
ShowGameCount = 1
InstallToDir = 2
GameSplit = 2
InstallPartitions = FFFFFFFD
PlaylogUpdate = 0
ParentalBlocks = FFFFFFFF
returnTo =
HomeMenu = 2
MultiplePartitions = 0
USBPort = 0
USBAutoMount = 1
BlockIOSReload = 2
WSFactor = 0.800
FontScaleFactor = 0.800
ClockFontScaleFactor = 1.000
EnabledCategories = 0
RequiredCategories =
ForbiddenCategories =
Wiinnertag = 0
WiinnertagPath = usb1:/apps/usbloadergx_r1281/
SelectedGame = -1
GameListOffset = 0
RememberLastGame = 0
sneekVideoPatch = 0
NandEmuMode = 0
NandEmuChanMode = 2
NandEmuPath = sd:/nand/
NandEmuChanPath = sd:/nand/
UseSystemFont = 1
Hooktype = 1
WiirdDebugger = 0
WiirdDebuggerPause = 0
ShowPlayCount = 0
bannerFavIcon = 4
LoaderMode = 9
SearchMode = 0
GameAspectRatio = 2
PointerSpeed = 0.18
UseChanLauncher = 0
AdjustOverscanX = 0
AdjustOverscanY = 0
TooltipDelay = 1500
GameWindowMode = 2
CacheBNRFiles = 1
BannerAnimStart = 0
BannerGridSpeed = 25.6
BannerZoomDuration = 30
BannerProjectionOffsetX = 0
BannerProjectionOffsetY = 0
BannerProjectionWidth = 608
BannerProjectionHeight = 470
GCBannerScale = 1.5
GameCubePath = sd:/games/
GameCubeSDPath = sd:/games/
GameCubeMode = 2
GameCubeSource = 2
MultiDiscPrompt = 0
DMLVideo = 0
DMLProgPatch = 0
DMLNMM = 1
DMLActivityLED = 0
DMLPADHOOK = 1
DMLNoDisc2 = 0
DMLWidescreen = 0
DMLScreenshot = 0
DMLJPNPatch = 0
DMLDebug = 0
NINDeflicker = 0
NINPal50Patch = 0
NINWiiUWide = 0
NINVideoScale = 0
NINVideoOffset = 0
NINRemlimit = 0
NINArcadeMode = 0
NINCCRumble = 0
NINSkipIPL = 1
NINBBA = 0
NINBBAProfile = 0
NINMCEmulation = 1
NINMCSize = 2
NINAutoboot = 1
NINSettings = 2
NINUSBHID = 0
NINMaxPads = 2
NINNativeSI = 0
NINOSReport = 0
NINLED = 0
NINLog = 0
DEVOMCEmulation = 1
DEVOWidescreen = 0
DEVOActivityLED = 0
DEVOFZeroAX = 0
DEVOTimerFix = 0
DEVODButtons = 0
DEVOCropOverscan = 0
DEVODiscDelay = 1
DEVOLoaderPath = sd:/apps/gc_devo/
NINLoaderPath = sd:/apps/Nintendont/
GCInstallCompressed = 0
GCInstallAligned = 1
PrivateServer = 0
CustomAddress = wiimmfi.de
URL_Banners =
https://banner.rc24.xyz/
URL_Covers2D =
https://art.gametdb.com/wii/cover/
URL_Covers3D =
https://art.gametdb.com/wii/cover3D/
URL_CoversFull =
https://art.gametdb.com/wii/coverfull/
URL_CoversFullHQ =
https://art.gametdb.com/wii/coverfullHQ/
URL_Discs =
https://art.gametdb.com/wii/disc/
URL_DiscsCustom =
https://art.gametdb.com/wii/disccustom/
URL_GameTDB =
https://www.gametdb.com/wiitdb.zip
URL_Cheats =
https://codes.rc24.xyz/txt.php?txt={gameid}
ProxyUseSystem = 1
ProxyUsername =
ProxyPassword =
ProxyAddress =
ProxyPort = 0