I did some modifications and added some extra functions in the file
What should I do to not lose these modifications in a future component update?
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If the Helper Class is loaded in a dynamic way, checking if it's already loaded, YES. You can override it.
Not with a HTML overrides, but with a System Plugin. You can create a System plugin, loading same Helper Class before the original one.
Please, check this related question: How to override core classes?