It seems like the issue you're facing with the custom help files in your toolbox is specific to your own toolbox and not affecting the toolboxes downloaded from Matlab Central. Here are a few suggestions to help you troubleshoot and resolve the problem:
1. Check the folder structure: Verify that the custom help files are placed in the correct location within your toolbox's folder structure. Make sure they are in the same location as before and haven't been unintentionally moved or deleted.
2. Verify XML files: Double-check the `info.xml` and `helptoc.xml` files in your toolbox. Ensure that they are correctly formatted and contain the necessary information to display the custom help files. It's possible that the deletion of the unused paths affected these files, so compare them with the versions you had before to ensure they are intact.
3. Clear MATLAB cache: MATLAB may cache the help files for performance reasons. Clearing the cache can help refresh the help system and display the updated custom help files. You can do this by running the following command in MATLAB's Command Window:
4. Update MATLAB path: Make sure that the paths to your toolbox and custom help files are correctly added to MATLAB's search path. You can check this by running the `path` command in MATLAB and verifying that the necessary paths are included.
5. Test on a clean installation: To further investigate the issue, you can try testing your toolbox on a clean installation of MATLAB. This will help determine if the problem is specific to your MATLAB environment or if it's related to the toolbox itself.
If none of these suggestions resolve the issue, it may be helpful to provide more specific details about the folder structure and contents of your toolbox, as well as any error messages or warnings you encounter.
To read more about the above mentioned suggestions kindly view the following documentations:
Hope this helps!