Weirdly later on the 23rd when I had a fresh install of 4.7.7 it went down again in the night with the same symptoms as 4.8.2. It then worked fine for the rest of the weekend which is the longest it has worked since I started having issues.
This morning I done a fresh install of 4.8.2 and it disconnected again later in the morning, during this outage I already had a spare router setup with my isp's pppoe details preconfigured so I took the wan cable from the flint 2 and plugged it into the spare router and it connected to the internet fine.
I noticed on my flint 2 that there didn't seem to be any indication of Pppoe authentication actually happening according to the logs. So I reset the trick I did here GL-MT6000 (Flint2) How change LAN2 - LAN5 port to WAN - #15 by cyph and I made eth1 the wan port and set lan2 back to Lan and br-lan and voila it started connecting perfectly fine.
Then I tried to set eth1 back to lan and lan2 back to wan and it wouldn't connect the internet, so maybe the new firmware changes the behaviour of how the ports are managed and how internet is connected?
I can send you logs later on via DM. I also noticed there's a few comments in that post about changing JSON files, to confirm I haven't touched those at all.