Cheers Sky. It's not worked though.
What ever was done actually resulted in a single chunk with two croppers in it and one chunk without a cropper at all.
They all turned to normal hoppers when mined and I cant place new croppers.
I tried placing more hoppers and removing them but still no luck.

Line 85 on checks to see if it was a crop hopper that was removed.

 

Yes, the working theory was that you still had the database entry present but not a physical crophopper. Which placing + breaking a regular hopper at the location marked by the entry should have resolved. Unfortunately this did not appear to be the case.

 

Sadly no, but it does reinforce my idea that if a cropperless chunk in copied in, then that chunk data will be copied as well allowing me to then place a new cropper.

 

That is likely the case.
Unless SB devs have attached it to the chunkdata, crop hopper data (location) would be in a separate database/file, unaffected by worldedit.

 

You should apply for Sb dev !!!!

 

Does Skyblock have anyone that could confirm and resolve this?

 

Noobcrew. Do you have anyone that can look at this.
Losses are getting up around $2 million since it was first reported.

 

Kerahna has had another go at copying a cropperless chunk over (Thanks Kera), but it doesn't copy the cropper data as I was still unable to place a cropper there.
Will definately need someone to look at the code and edit it there.
Noobcrew. I'm hoping you can keep me informed so I know I'm not forgotten. Losses are around $200,000 per day.

 

Problem solved!

I was looking at the code that ~Sky~ linked and figured, I just needed to break the croppers in those chunks.
Sure, I couldn't see them, but they were there, at least the code said they were there.
I didn't know where they were but I knew the 'y' level they were placed at, so I filled that level with cobble and broke it all.
Low and behold, when I broke the cobble where the code believed the cropper to be, it dropped the cropper!
After that, I was able to place it down again .

Now I just need to move some water sources and lighting, harvest and replant everything and I'm all good.

Thanks again to Kerahna a for the help.