Getting 404 on subfolders multisite setup

Recently there was an issue with htaccess being created in the uploads folders, I haven't updated or installed anything and now when I create subsites I just get a 404 when I try to access the subsites with subfolder setup.

I'm using the domain mapping option explained in the WordPress docs, which requires only to manually chage the site URL to the domain I will map and adding the domain as addon, the sites that are mapped work but the subsites that are using the subdirectory just throw a 404 error (admin area or front-end).

Tried clearing cache with a plugin but got the same issue.

This is the main domain of the multi-site http://lifestyleadvisers.net.au
This is one of the subsites http://lifestyleadvisers.net.au/devsite/wp-admin/

Thanks in advance!