Thus, the file was deleted from CM, but there is still a link to it on the CD (according to the CD, it still exists and is still used by something).
You should publish the page after removing 1001, but before adding 1002. This should remove the link from the CD database. Then you should be fine to add 1002 and publish the page again.
[EDIT] Sorry, just now read that you say that you did not publish everything. Clearly, no, since there is still a link to it ... opening a virtual machine will return with updates.
[EDIT2] Still don't understand how it remains a conflict if you cancel the publication, but this is what I observe on my server:
- Add binary to page, publish
- Link added to table "REFERENCE_ENTRIES" on CD
- Remove binary from page, publish
- Link removed from table "REFERENCE_ENTRIES", binary removed.
- Unpublish the page (after re-adding binaries, republishing)
- Link removed from table "REFERENCE_ENTRIES", binary removed.
So, in my case, I see what I would expect. Try publishing the page after deleting the binary, and if possible, check that the REFERENCE_ENTRIES table is in.
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