Don't delete everything - if you do that, you lose part of your configuration as well, which will make it hard to run Pi-hole.
Pi-hole's core component (piholeFTL based on dsnmasq) is configured via a set of files under /etc/dnsmasq.d/.
Pi-hole's default configuration options as well as blocklists and long-term database are stored under /etc/pihole/.
Let's take a look at what's in this folders first, so we could figure which files can go and which not (if it is a file issue at all).
That way, we could also verify that you indeed exposed the right folders.
EDIT: Sorry for updating this repeatedly after posting - I just wanted to get the Don't delete out as quickly as possible 
P.S.: For an overview where Pi-hole keeps what, refer to What files does Pi-hole use?