All Links Point To Root – Error

This is the case for a number of my sites, in the one hosting account,

I have a root domain with a WP installation, and in that domain is a folder with another wp installation.

Everything was fine, until recently, when I noticed when clicking the links in the folder, go to the root domain as a 404 page, as if the folder didn’t exist (except for the homepage of the folder works as it should)

Same issue my wp multisite, the multisites links all go to the root folder.

Everything was all working fine, and then they were not, but not sure if the issues across all domains happened at the same time or if they happened at different times.

Could this just be malware issue?