How to remove all items in the end dimension without chunks being loaded?

It's quite easy: you go to NBTExplorer, find your world in appdata or wherever. Go to DIM1, which is the end folder, and find the chunk that is lagging your world. Now seeing the video I used this design so the spawn platform from my personal world(s) will always spawns at r.0.0.mca chunk 6, 0; this is where the platform will be and where the entities will be located, so all you have to do in this chunk is delete all the entities.

Note that in this chunk any entity will be deleted: item frames, minecarts, armor stands, etc. Anything that is entity based will be deleted. So assuming you don't have anything like that deleting the items is probably your best bet. Just go to entities and delete the entire archive so every entry of items. Now, depending on how many items there are, this could lag NBTExplorer, so be careful of that. As long as the items are not exceeding probably 1-10 million items, it should be okay - it will be incredibly slow but it should eventually get there.

Anyway, delete all the entities and hit Save once that is done: that chunk you deleted all the entities in should be fixed.

Note though, that if you get the wrong folder for the Overworld or the Nether then those entities will be gone potentially causing corruption, so I highly recommend a backup and then trying this. It's unlikely it will cause chunk errors but it's a possibility to take into consideration so just use at your own risk. Anyway, this should fix the end and remove the crashing.

There is no way to alter a chunk without loading it first. At least not "from within minecraft".

What you could try to do, if the end dimension as it currently is is super important to you and there is no way you just delete and regenerate it entirely would be to manually edit the chunk data with an NBT (=the format of the save files) editor like this one. (Or just search Google for "minecraft nbt editor", there are multiple different programs available.)

The format in which the data is stored is explained in detail in this article from the Minecraft Wiki.

But this looks to me like a HUGE pain in the butt, so I would only recommend it, if you absolutely need to restore the end dimension.

Also, it's a bit of a stupid question by myself, but don't you have any backups? If you run a Bukkit / Spigot server, it's pretty easy to set up your own little backup script that just copies the world saves to a different location in a regular interval. You'd just have to start the backup script when you start the server itself.

I'd generally recommend for the future, that you back up your world so you can revert things that went wrong, or recover your world after a crash.