Add mod using the command or manually add a metadata file pointing to a file download URL.
Put metadata file outside of your mods-folder.
Do "packwiz refresh" (packwiz will remove the "metafile = true" from metadata files in "index.toml" when that metadata is outside of your defined mods-folder)
At this point you should really go and manually add the "metafile = true" setting to your metadata in "index.toml" if you want the file to be downloaded, but in this case let's say you forgot to do this.
Start client or server that points to your "pack.toml" and check the folders. You'll see that the mods or files are not there but there're metadata files (.toml) instead.
You realized your mistake but there's nothing to be worried about, you only need to go and add "metafile = true" to the metadata files in "index.toml" and that's it, right?
Add "metafile = true" setting to your metadata files in "index.toml".
Start client or server and check de folders, the metadata files (.toml) are still there even if you already specified them to be "metafile = true" in "index.toml"
Tell all your users to please delete a folder on their .minecraft folder.
How to reproduce: