As my server always experiences obscure chunk problems. I'd like to say that I've become experienced in dealing with them. To all who share the same struggles, here's your fix!
First Step: Check for corruption
Run Region Fixer, this program works for every Minecraft version since the world file formats remains the same (as of posting this). This works on linux as well, check his installationand usage guide. If you're with a host, you'll have to download the world and run it on your computer.
Now if this solved your problem. Great! You're done!
Step Two: But if it didn't
Looks at your crash log. Does it say:
Description: Exception in server tick loop
If it does, this is your fix! If not, I'm not sure what to tell you...
Download World Util for 1.10.2 and add it to your mods folder. Now launch your server and execute
/worldutils tileticks remove-invalid rescan
That should automatically detect and remove any invalid blocks. (I got these invalid block ids after upgrading from Pixelmon 5 beta 9 to 12)
If you want to find out the culprit that's causing your demise
/worldutils tileticks find-invalid rescan
/worldutils tileticks find-invalid list
this will create a log inside /config/worldutils that will detail every tiletick's id and you can find which one appears wrong. (For me, I had pixelmon:dawnduskore which is the wrong id for dawn dusk ore)
If you have any questions about this process, please ask away! You can also feel free to @DiamondArrow on the Pixelmon Discord
Thanks to everyone on Pixelmon's Discord helping me along the way!
And a big thanks to masa (creator of world util) troubleshooting and updating his mod for me <3