upgrade issue

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upgrading from 5.4.2.1 to 5.4.2.2 I get a fault that says the script is missing some files and that I should start from scratch.

Can I reinstall over the existing without losing the content of my website?

or when it says "start from scratch" it really means from scratch?

Everything is working just fine, was just doing the routine update.

thanks

ARROC.com