Hi,
we're upgrading our server from the MC 1.10.2 to the MC 1.12.2.
The server 1.10.2 is running for two years without problems. It's running on SpongeForge spongeforge-1.10.2-2281-5.2.0-BETA-2610 and forge-1.10.2-12.18.3.2281-universal.
We use the AppliedEnergistics appliedenergistics2-rv4-stable-1 on the server.

Now we created a new server, based on MC 1.12.2. We built it on the latest version of SpongeForge: spongeforge-1.12.2-2838-7.1.9 and Forge: forge-1.12.2-14.23.5.2838-universal. We put there the latest Applied Energistics: appliedenergistics2-rv6-stable-7.

We've many other mods on our server including IC2, Forestry, RailCraft, IntegratedDynamics etc.

We copied the whole world folder with all worlds to the new server 1.12.2. Then we started the new server. It asked for /fml confirm - the confirmation to remove some items/blocks which doesn't exist. After confirmation server started.

Now the problem description:
Every mods seems working, some blocks were removed, especially a blocks from the IntergatedDynamics and the ProjectRed mods.
Our AE2 networks are working, but all storage cells are empty and all crafting patterns placed into interfaces next to molecular assemblers were removed and all Export/import bus configurations are gone. It seems that the AE2 has been completely wiped out.

Looking into debug log, I found these lines, a lot of them:
[17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:2268L,id:"minecraft:gravel",Count:0b,Damage:0s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:182L,id:"minecraft:gold_ore",Count:0b,Damage:0s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:7518L,id:"minecraft:iron_ore",Count:0b,Damage:0s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:32L,id:"minecraft:golden_rail",Count:0b,Damage:0s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:101L,id:"minecraft:brick_block",Count:0b,Damage:0s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:581L,id:"minecraft:obsidian",Count:0b,Damage:0s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:372L,id:"minecraft:fence",Count:0b,Damage:0s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:9L,id:"minecraft:iron_bars",Count:0b,Damage:0s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:12L,id:"minecraft:quartz_block",Count:0b,Damage:0s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:6L,id:"minecraft:quartz_block",Count:0b,Damage:1s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:204921L,id:"minecraft:log2",Count:0b,Damage:1s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:1L,id:"minecraft:bow",Count:0b,Damage:23s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:5003L,id:"minecraft:coal",Count:0b,Damage:0s,Req:0L} from storage cell because the associated item type couldn't be found. [17:06:48] [Server thread/WARN] [AE2:S]: Removing item {Craft:0b,Cnt:49L,id:"minecraft:diamond",Count:0b,Damage:0s,Req:0L} from storage cell because the associated item type couldn't be found.

Please what's wrong? Can you help me? We'd like to upgrade to the 1.12.2, but this issue is a big problem. We don't want to lost all our items/crafting recipes and configurations.
Can you help us, please?
Is there anything we can do to solve the problem?

Note that we use the Nucleus plugin (for Sponge) to manage multiple worlds.

Thank you very much.
Fipil

Upgrading major minecraft versions is simply not supported.

Really? Is this all information you can provide? Would you be so kind and give me some options or workarounds? Is there anything what can I do to transfer our items/recipes from your AE1.10 to AE1.12?
I'm a programmer, so can I for example write some simple server mod (Forge) which can store items/recipes to some file, then use the mod in our 1.12 server to restore items? Can you point me to some examples how can I do it? How can my mod interact with AE? Or is there any other way?
Thank you.

Pretty much yes. I cannot even remember how 1.10 actually stored its data, just some basic recollection about 1.12 forcing us to completely break it due to how forge handles item caps.
Maybe even some vanilla changes on top. There were some breaking changes during 1.11 or 1.12 which messed up quite a bit of itemstack handling.

This would most likely also apply to any other mod, so it would not just need a convert from 1.10 cells to 1.12 cells, but also a converter for every stored item as long as these are not the most trivial blocks. E.g. for anything storing energy/items/etc and moving from normal NBT to item caps in 1.12.

Okay. That's quite bad news, but I understand. Thank you very much for explanation.

Technically minecraft has a way to perform migrations on itemstacks, but that is really lacking outside of plain vanilla content.

E.g. every single mod out there has to write their own explicit support for it. Otherwise anything not stored inside the player inventory, vanilla chests (or other vanilla storage blocks) won't be converted.
It only supports a single version, so e.g. anything item caps based cannot be really converted without probably breaking other transformations. Or if it would even work in some cases like bags/containers stored inside other bags/containers.
Knowing forge, once it works to some degree and gets more widely adopted it will break down in terms of performance for chunkloading.

As well as requiring at least one more breaking change on our side. Otherwise any transformer will most likely break our itemstacks without us being able to recover from it.