I recently create another folder for Minecraft, in another HDD instead of the roaming where I already have an instance, so I copied all the files I wanted into the new one.

My schematic folder has multiples folder inside to keep everything in order and I can load all of them without issue, but if I save a schematic inside a folder, it doesn't appear if I try to load it. But if the schematic is save in the root directory, there is no issue.

I never had this issue while playing with the default instance location in the roaming folder, it only started when I created the 2nd instance.

Fabric 0.39.2
Litematica 1.17.1-0.0.0-dev.20210713.103711
Malilib 1.17.1-0.10.0-dev.24

Check the paths your schematic saving file browser is in, vs. the Load Schematics menu's file browser. If you also copied over the Litematica configs, then the new instance might still be pointing to the schematic directory in the old location, as all of the different file browser menus in Litematica store the last directory they were in. If you click the Root Directory button in the file browser, then it will jump to the current root .minecraft/schematics/ directory, in case it was currently pointing to the other instance's equivalent schematics directory.

You can also kind of see this in the path bar at the top - does it have the full absolute pat starting from C:\Users\whatever (in which case it's not under the current schematics directory), or does it just start with schematics.

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