I've had this same problem this evening. After booting this Mac on a Linux Mint live CD for a couple of hours, once I was back on macOS Pi-hole insisted that my hostname was still mint.lan for queries that were being generated right now. I had the same IP for both sessions since it's the same wired network adapater. Pi-hole is the DHCP.
I tried deleting it from the Network view and it came right back as mint.lan. I also tried the Flush network table option you listed and it made no difference.
I then took the nuclear option and rebooted the Pi-hole and that did fix it. Interestingly the Long-term data showed recent queries as mint.lan and then changing to the Mac hostname after the relevant PTR request from localhost (the Pi-hole) for the Mac's reverse IP.
The entire Query Log last 100 entries however showed the Mac hostname for everything. Presumably because the Query Log is populated from the Long-term data on boot.
Long-term data Query shows Mint hostname
Main Query Log shows same transactions using current Mac hostname
Would I be right to say that it was the PTR request for the Mac which actually "fixed" the problem? Image below from Long-term data, since main Query Log now shows correct hostnames where it was incorrect before, as shown above. Dashboard also no longer has any record of mint.lan.
