The Route implementation process involves duplicating the current theme installed on Shopify, then adding the code to the duplicate. After the implementation is done, the theme is then pushed live and takes place of the pre-existing theme.
Very rarely, this duplication process does not fully execute in Shopify, which results in a fragmented version of the store, often resulting in the menu becoming limited or disappearing entirely.
Fortunately, the main theme is unaffected and the store's code is still intact–it just needs to be pushed live again.
If this, or something similar, has occurred in your store please contact our support team immediately at this link, where our support staff will respond within one business day. If this is an urgent matter, please reach out to us on our chat.