1. Locate the Modrinth App Data Folder
Navigate to your operating system's hidden application data directory to find where Modrinth stores instance files. On Windows, press Win + R, type %appdata%, and hit enter to open the roaming folder. Look for a folder named modrinth or similar within this directory to access stored instances. This step matters because the visible launcher list often references cached data that survives simple deletion attempts. You will find a subfolder containing JSON files that track instance metadata and download paths.
2. Check the Instances Subdirectory First
Open the instances folder inside the Modrinth directory to see if the problematic entry exists as a direct folder. Delete the entire folder corresponding to the stubborn instance using your file manager or command line. Ensure you close the Modrinth launcher completely before attempting this removal to avoid file lock issues. This works if the instance is stored locally rather than being pulled from a persistent cache or sync service. The folder disappears from your file explorer immediately after you confirm the deletion action.
3. Clear the Launcher Cache and Settings
Search for any cache or config folders within the Modrinth application directory that might retain instance references. Delete files named instance_cache.json, settings.json, or similar files that track downloaded content history. Restart your computer after clearing these files to ensure no background processes hold onto old data. This step addresses cases where the launcher reloads deleted instances from a local database instead of the file system. You will notice the launcher takes longer to load initially as it rebuilds its internal index.
4. Verify Account Sync and Cloud Settings
Log into your Modrinth account on the website to check if cloud sync is enabled for your instances. Disable any synchronization features that might be restoring deleted instances from a remote backup automatically. Remove the instance from the web dashboard if it appears in your library there as well. This matters because cloud syncing can override local deletions if the server thinks the instance still belongs to your account. The instance no longer appears in the web library after you confirm the removal online.
5. Reinstall the Modrinth Launcher
Uninstall the current Modrinth launcher completely from your system using the standard uninstaller or package manager. Delete any remaining folders in the appdata directory to ensure all configuration files are wiped. Download the latest version of the launcher from the official website and install it fresh. This step is necessary if corrupted configuration files are causing the launcher to misread deletion commands repeatedly. The launcher starts with a clean slate and does not populate the deleted instance in your list.
6. Manually Edit the Instance Registry File
Open the instances.json or registry file inside the Modrinth config folder using a text editor like Notepad. Search for the name or ID of the stubborn instance within the file content. Remove the specific line or block of text that references this instance from the file. Save the file and close the text editor before reopening the launcher to apply changes. This directly edits the database that tells the launcher what instances exist regardless of folder presence.
7. Check for Symbolic Links or Mount Points
Inspect your file system for symbolic links that might point to the deleted instance folder elsewhere on your drive. Use the command line to list symbolic links in your Modrinth directory and remove any pointing to the old path. This issue occurs if you previously moved instance folders and created links instead of copying files directly. The launcher follows these links and treats the target location as a valid instance source. You will confirm the link is gone by running the ls -la command again in that directory.
8. Prevent Future Recurrence with Backup Control
Create a backup of your Modrinth config folder after successfully cleaning the instance list to restore it if issues return. Avoid downloading instances from unverified sources that might carry hidden metadata causing sync conflicts. Regularly check your account settings to ensure cloud sync matches your local preferences for instance management. This proactive measure saves time by allowing quick restoration of a known good state if the problem resurfaces. A zip file of your config folder now exists on your desktop for future recovery.