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I made a Minecraft map in worldpainter, exported it and got it on a server, then we built some mines in a small part of the map. However, we found that some parts of the map probably got corrupted and there were a lot of empty chunks.

I still have the unbuilt version of map and want to just add the missing chunks back to the map with builds, and MCEdit is giving me a lot of errors.

Is there any other way of doing it?

this is how the missing chunk map look

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I'd suggest - if your custom builds only occupy a relatively small volume; significantly smaller than the error chunks - to use Litematica to mark them and generate schematics of them in the corrupted world (and write down the coords of each area you make the litematic of), then make a copy of the 'pristine' custom world, substitute the server's world with it, verify it's fine this time (no chunk errors), then use litematica's "paste" function (after aligning the placements of the schematics to their original positions) to restore your builds.

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