I'm rather new to uploading/editing, but I recently found that a picture (post #990112) had been deleted on Pixiv, but was reuploaded recently. I wasn't sure if I should just change the source to the new source, or upload the new one (they're seemingly identical) and list the old one as a child post.
I think in this case you'd probably change the source address of the original to the new address. The MD5sum of the reupload is b69d22e95876151b5d921b3894e6f478, which is identical to post #990112 (b69d22e95876151b5d921b3894e6f478.jpg). Though I haven't really worked with this stuff, so I'd still have to have someone verify my results and conclusion.
For this case, the hashes match, so I've changed the source (and updated the artist entry).
You can check the hashes by saving the Pixiv image to your hard drive, then uploading it from there to a site like this, and comparing the result to the Danbooru filename.
If that's too much trouble or it's an image you wouldn't mind uploading yourself, I recommend just trying uploading it. If the hashes match, Danbooru will just redirect you to the old page, in which case you'd just change the source. If the upload succeeds, something is different about it, so make the new post the parent.
If the hashes don't match and you don't want to reupload it, leave the source alone and just note the location of the new version in the comments.