HELP!

I've been playing with this bug with my brother for about 3 years on and off on our creative world which was created about 6 years ago. We've been able to manage it because it mainly only made the underground into Swiss cheese (and it was producing some pretty cool looking patterns). But as if of this week it finally started to eat our buildings as well. We have WorldEdit (an old version) and ClearLag installed. It's not taking up too much of my computers RAM, its running on 14% more or less all the time. Nothing is showing up in the console except for a few "Did the system change or did the system overload - skipping x tick". Something like that its not very consistent. The server have crashed a few times lately for seemingly no obvious reason. I can paste the crash texts if demanded I can't get much out of them myself.

Screenshots:
https://www.dropbox.com/s/8h1wcnaaktyd550/2017-03-23_04.50.02.png?dl=0 (Random holes popping up on ground level).https://www.dropbox.com/s/d5a7vuflbef436x/2017-03-23_04.50.16.png?dl=0 (It always glows at this spot there are no blocks nearby that emit light. It has been like this for years).
https://www.dropbox.com/s/3d28fdpnr0wic72/2017-03-23_04.51.31.png?dl=0 (The pattern is very clear underground and NO we did not dig these tunnels ourselves!)(Also I want to add that we spawned above a stronghold 7 dungeons and 2 abandoned mine shafts unfortunate seeing how we're playing on creative).
https://www.dropbox.com/s/h5cez0l3zx0l83m/2017-03-23_04.51.17.png?dl=0 (The further away you go the less the bug occurs but with more time spent in that area it sees the same fate in the end).
https://www.dropbox.com/s/2p0xvo4rgmnp4q5/2017-03-23_04.50.26.png?dl=0 (One of my buildings before the bug ate it today).
https://www.dropbox.com/s/e5tcyg38lomgj3w/2017-03-23_04.21.52.png?dl=0 (Oh God, afterwards. If you reach long enough you could see the pattern occurring in the destruction of this building as well. Also this part of the city is one of the oldest).

Hopefully someone answers this call for help. Its gotten pretty bad. I will try to update to the latest WorldEdit tomorrow morning all answers are appreciated!

Also it's worth to mention that once during a Minecraft patch long ago when we joined the server all the chunks were reset with all the buildings and human interference were removed. Being the bright kid that I was I made sure to always save a backup which is the world we've been playing on since then. This was about 4-6 years ago and I do not remember which patch it was that caused it. But the world file got corrupted. Again it was another world still worth a mention.

Also this is a follow-up thread from this one created 2015 https://www.spigotmc.org/threads/random-disappearing-blocks-since-1-8-craftbukkit.54548/ It looks like we had the same bug.