The instructions you have linked to seems to modify the first partition on the flash drive. This changes the partition from an EFI type to a HFS+ type. This modification should not have been altered when Windows was installed. The only plausible explanation I can deduce is you made the modification to the first partition of the internal drive instead.
You should be able to make repairs by executing the steps starting at the beginning of section titled "The manual boot"
Just as a personal note. The author of the linked site has posted a unnecessarily complex solution to a problem that no longer exists with the introduction of Ubuntu 18.