When attempting to upgrade a server from 0.1.12 to 0.2.1, I receive the below error once the server has loaded.

What I've tried:
Removing the FTBChunks folder from world
Removing all folders/files except the world and pulling the files from the 0.2.1 server pack

This does not occur when creating a new world on singleplayer or multiplayer. This crash also occurs when loading the world file as a singleplayer world. I can attach the full crash log from the server if needed.

net.minecraft.ReportedException: Exception ticking world at net.minecraft.server.MinecraftServer.m_5703_(MinecraftServer.java:897) ~[server-1.20.1-20230612.114412-srg.jar%23793!/:?] {re:mixin,pl:accesstransformer:B,re:computing_frames,pl:accesstransformer:B,re:classloading,pl:accesstransformer:B,pl:mixin:APP:kubejs-common.mixins.json:MinecraftServerMixin,pl:mixin:APP:kubejs-common.mixins.json:inject_resources.MinecraftServerMixin,pl:mixin:APP:modernfix-common.mixins.json:perf.dedicated_reload_executor.MinecraftServerMixin,pl:mixin:APP:balm.mixins.json:MinecraftServerMixin,pl:mixin:APP:ae2.mixins.json:spatial.MinecraftServerMixin,pl:mixin:APP:citadel.mixins.json:MinecraftServerMixin,pl:mixin:APP:dankstorage.mixins.json:MinecraftServerAccess,pl:mixin:APP:gtceu-common.mixins.json:MinecraftServerMixin,pl:mixin:A} at net.minecraft.server.dedicated.DedicatedServer.m_5703_(DedicatedServer.java:273) ~[server-1.20.1-20230612.114412-srg.jar%23793!/:?] {re:mixin,pl:accesstransformer:B,re:computing_frames,pl:accesstransformer:B,re:classloading,pl:accesstransformer:B,pl:mixin:APP:mixins/common/nochatreports.mixins.json:server.MixinDedicatedServer,pl:mixin:APP:tombstone.mixins.json:DedicatedServerMixin,pl:mixin:A} at net.minecraft.server.MinecraftServer.m_5705_(MinecraftServer.java:814) ~[server-1.20.1-20230612.114412-srg.jar%23793!/:?] {re:mixin,pl:accesstransformer:B,re:computing_frames,pl:accesstransformer:B,re:classloading,pl:accesstransformer:B,pl:mixin:APP:kubejs-common.mixins.json:MinecraftServerMixin,pl:mixin:APP:kubejs-common.mixins.json:inject_resources.MinecraftServerMixin,pl:mixin:APP:modernfix-common.mixins.json:perf.dedicated_reload_executor.MinecraftServerMixin,pl:mixin:APP:balm.mixins.json:MinecraftServerMixin,pl:mixin:APP:ae2.mixins.json:spatial.MinecraftServerMixin,pl:mixin:APP:citadel.mixins.json:MinecraftServerMixin,pl:mixin:APP:dankstorage.mixins.json:MinecraftServerAccess,pl:mixin:APP:gtceu-common.mixins.json:MinecraftServerMixin,pl:mixin:A} at net.minecraft.server.MinecraftServer.m_130011_(MinecraftServer.java:661) ~[server-1.20.1-20230612.114412-srg.jar%23793!/:?] {re:mixin,pl:accesstransformer:B,re:computing_frames,pl:accesstransformer:B,re:classloading,pl:accesstransformer:B,pl:mixin:APP:kubejs-common.mixins.json:MinecraftServerMixin,pl:mixin:APP:kubejs-common.mixins.json:inject_resources.MinecraftServerMixin,pl:mixin:APP:modernfix-common.mixins.json:perf.dedicated_reload_executor.MinecraftServerMixin,pl:mixin:APP:balm.mixins.json:MinecraftServerMixin,pl:mixin:APP:ae2.mixins.json:spatial.MinecraftServerMixin,pl:mixin:APP:citadel.mixins.json:MinecraftServerMixin,pl:mixin:APP:dankstorage.mixins.json:MinecraftServerAccess,pl:mixin:APP:gtceu-common.mixins.json:MinecraftServerMixin,pl:mixin:A} at net.minecraft.server.MinecraftServer.m_206580_(MinecraftServer.java:251) ~[server-1.20.1-20230612.114412-srg.jar%23793!/:?] {re:mixin,pl:accesstransformer:B,re:computing_frames,pl:accesstransformer:B,re:classloading,pl:accesstransformer:B,pl:mixin:APP:kubejs-common.mixins.json:MinecraftServerMixin,pl:mixin:APP:kubejs-common.mixins.json:inject_resources.MinecraftServerMixin,pl:mixin:APP:modernfix-common.mixins.json:perf.dedicated_reload_executor.MinecraftServerMixin,pl:mixin:APP:balm.mixins.json:MinecraftServerMixin,pl:mixin:APP:ae2.mixins.json:spatial.MinecraftServerMixin,pl:mixin:APP:citadel.mixins.json:MinecraftServerMixin,pl:mixin:APP:dankstorage.mixins.json:MinecraftServerAccess,pl:mixin:APP:gtceu-common.mixins.json:MinecraftServerMixin,pl:mixin:A} at java.lang.Thread.run(Thread.java:833) ~[?:?] {re:mixin} Caused by: java.lang.NullPointerException: Cannot invoke "it.unimi.dsi.fastutil.longs.LongArrayList.getLong(int)" because "this.wrapped" is null at it.unimi.dsi.fastutil.longs.LongOpenHashSet$SetIterator.nextLong(LongOpenHashSet.java:545) ~[fastutil-8.5.9.jar%2390!/:?] {} at it.unimi.dsi.fastutil.longs.LongCollection.removeIf(LongCollection.java:274) ~[fastutil-8.5.9.jar%2390!/:?] {re:computing_frames} at it.unimi.dsi.fastutil.longs.LongCollection.removeIf(LongCollection.java:306) ~[fastutil-8.5.9.jar%2390!/:?] {re:computing_frames} at it.unimi.dsi.fastutil.longs.AbstractLongCollection.removeIf(AbstractLongCollection.java:159) ~[fastutil-8.5.9.jar%2390!/:?] {re:computing_frames} at net.minecraft.world.level.entity.PersistentEntitySectionManager.m_157577_(PersistentEntitySectionManager.java:251) ~[server-1.20.1-20230612.114412-srg.jar%23793!/:?] {re:classloading,pl:accesstransformer:B} at net.minecraft.world.level.entity.PersistentEntitySectionManager.m_157506_(PersistentEntitySectionManager.java:270) ~[server-1.20.1-20230612.114412-srg.jar%23793!/:?] {re:classloading,pl:accesstransformer:B} at net.minecraft.server.level.ServerLevel.m_8793_(ServerLevel.java:355) ~[server-1.20.1-20230612.114412-srg.jar%23793!/:?] {re:mixin,pl:accesstransformer:B,xf:fml:libx:level_load,re:classloading,pl:accesstransformer:B,xf:fml:libx:level_load,pl:mixin:APP:cupboard.mixins.json:ServerAddEntityMixin,pl:mixin:APP:betterendisland.mixins.json:ServerLevelMixin,pl:mixin:APP:kubejs-common.mixins.json:ServerLevelMixin,pl:mixin:APP:modernfix-common.mixins.json:bugfix.chunk_deadlock.ServerLevelMixin,pl:mixin:APP:modernfix-common.mixins.json:perf.cache_strongholds.ServerLevelMixin,pl:mixin:APP:supplementaries-common.mixins.json:ServerLevelMixin,pl:mixin:APP:corgilib.mixins.json:MixinServerLevel,pl:mixin:APP:hyperbox.mixins.json:ServerLevelMixin,pl:mixin:APP:ad_astra-common.mixins.json:ServerLevelMixin,pl:mixin:APP:aether.mixins.json:common.accessor.ServerLevelAccessor,pl:mixin:APP:citadel.mixins.json:ServerLevelMixin,pl:mixin:APP:observable.common.json:ServerLevelMixin,pl:mixin:APP:betterdeserttemples.mixins.json:ServerLevelMixin,pl:mixin:APP:enhancedcelestials.mixins.json:MixinServerWorld,pl:mixin:APP:create.mixins.json:accessor.ServerLevelAccessor,pl:mixin:APP:betterendisland.mixins.json:EndergeticExpansionMixins,pl:mixin:A} at net.minecraft.server.MinecraftServer.m_5703_(MinecraftServer.java:893) ~[server-1.20.1-20230612.114412-srg.jar%23793!/:?] {re:mixin,pl:accesstransformer:B,re:computing_frames,pl:accesstransformer:B,re:classloading,pl:accesstransformer:B,pl:mixin:APP:kubejs-common.mixins.json:MinecraftServerMixin,pl:mixin:APP:kubejs-common.mixins.json:inject_resources.MinecraftServerMixin,pl:mixin:APP:modernfix-common.mixins.json:perf.dedicated_reload_executor.MinecraftServerMixin,pl:mixin:APP:balm.mixins.json:MinecraftServerMixin,pl:mixin:APP:ae2.mixins.json:spatial.MinecraftServerMixin,pl:mixin:APP:citadel.mixins.json:MinecraftServerMixin,pl:mixin:APP:dankstorage.mixins.json:MinecraftServerAccess,pl:mixin:APP:gtceu-common.mixins.json:MinecraftServerMixin,pl:mixin:A} ... 5 more

It seems I was able to stop the crashing by doing the following:

1. Restore a backup from 0.1.21
2. Upgrade to 0.2.0
3. Upgrade to 0.2.1

It seems that upgrading directly from 0.1.21 to 0.2.1 causes corruption of the world